[med-svn] [Git][med-team/igv][upstream] New upstream version 2.15.4+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sat Jan 7 13:36:43 GMT 2023
Pierre Gruet pushed to branch upstream at Debian Med / igv
Commits:
0d90726e by Pierre Gruet at 2023-01-06T22:20:40+01:00
New upstream version 2.15.4+dfsg
- - - - -
25 changed files:
- src/main/java/org/broad/igv/batch/CommandExecutor.java
- src/main/java/org/broad/igv/batch/CommandListener.java
- src/main/java/org/broad/igv/feature/genome/Genome.java
- src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
- src/main/java/org/broad/igv/feature/tribble/MUTCodec.java
- src/main/java/org/broad/igv/oauth/OAuthProvider.java
- src/main/java/org/broad/igv/prefs/Constants.java
- src/main/java/org/broad/igv/prefs/PreferencesManager.java
- src/main/java/org/broad/igv/sam/AlignmentTrack.java
- src/main/java/org/broad/igv/track/BlatTrack.java
- src/main/java/org/broad/igv/track/TrackLoader.java
- src/main/java/org/broad/igv/ui/IGV.java
- src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java
- src/main/java/org/broad/igv/ui/color/ColorUtilities.java
- src/main/java/org/broad/igv/util/GoogleUtils.java
- src/main/java/org/broad/igv/util/HttpUtils.java
- src/main/java/org/broad/igv/util/blat/BlatClient.java
- src/main/java/org/broad/igv/variant/VariantTrack.java
- src/main/resources/org/broad/igv/prefs/preferences.tab
- src/test/java/org/broad/igv/ui/color/ColorUtilitiesTest.java
- − test/batch/exit.txt
- test/batch/multiple_bams.txt
- test/batch/path_with_spaces.txt
- + test/data/mut/tcga_20080711_phase1_filtered_nonsilent.mut
- test/web/StaticLinkExamples.html
Changes:
=====================================
src/main/java/org/broad/igv/batch/CommandExecutor.java
=====================================
@@ -36,7 +36,6 @@ import org.broad.igv.feature.Range;
import org.broad.igv.feature.RegionOfInterest;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.GenomeManager;
-import org.broad.igv.oauth.OAuthUtils;
import org.broad.igv.logging.LogManager;
import org.broad.igv.logging.Logger;
import org.broad.igv.prefs.Constants;
@@ -104,7 +103,7 @@ public class CommandExecutor {
log.debug("Executing: " + commandLine);
try {
if (args.size() == 0) {
- return "Empty command string";
+ return result;
}
String cmd = args.get(0).toLowerCase();
@@ -207,7 +206,7 @@ public class CommandExecutor {
FrameManager.incrementZoom(-1);
} else if ("oauth".equals(cmd) || cmd.equalsIgnoreCase("setaccesstoken")) {
HttpUtils.getInstance().setAccessToken(param1, param2);
- } else if(cmd.equals("clearaccesstokens")) {
+ } else if (cmd.equals("clearaccesstokens")) {
HttpUtils.getInstance().clearAccessTokens();
} else if (cmd.equalsIgnoreCase("sortByAttribute")) {
result = sortByAttribute(args);
@@ -623,25 +622,14 @@ public class CommandExecutor {
return result;
}
- String genomePath = genomeID;
- if (!ParsingUtils.fileExists(genomePath)) {
- String workingDirectory = System.getProperty("user.dir", "");
- genomePath = FileUtils.getAbsolutePath(genomeID, workingDirectory);
- }
- if (ParsingUtils.fileExists(genomePath)) {
- try {
- GenomeManager.getInstance().loadGenome(genomePath, null);
- } catch (IOException e) {
- result = "ERROR: Could not load genome: " + genomeID;
- MessageUtils.showMessage(result);
- }
-
- } else {
- result = "ERROR: Could not locate genome: " + genomeID;
+ String genomePath = resolveFileReference(genomeID);
+ try {
+ GenomeManager.getInstance().loadGenome(genomePath, null);
+ } catch (IOException e) {
+ result = "ERROR: Could not load genome: " + genomeID;
MessageUtils.showMessage(result);
}
-
return result;
}
@@ -714,130 +702,145 @@ public class CommandExecutor {
String sortTag,
boolean dup) {
- boolean isDataURL = ParsingUtils.isDataURL(fileString);
+ boolean currentBatchSetting = Globals.isBatch();
+ try {
+ // Temporarily switch to batch mode to force synchronization of load followed by possible sort
+ Globals.setBatch(true);
+
+ boolean isDataURL = ParsingUtils.isDataURL(fileString);
+
+ List<String> files = isDataURL ? Arrays.asList(fileString) : breakFileString(fileString);
+ List<String> indexFiles = isDataURL ? null : breakFileString(indexString);
+ List<String> coverageFiles = breakFileString(coverageString);
+ List<String> names = breakFileString(nameString);
+ List<String> formats = breakFileString(formatString);
+ if (names != null && names.size() != files.size()) {
+ return "Error: If file is a comma-separated list, names must also be a comma-separated list of the same length";
+ }
+ if (indexFiles != null && indexFiles.size() != files.size()) {
+ return "Error: If file is a comma-separated list, index must also be a comma-separated list of the same length";
+ }
+ if (isDataURL && formatString == null) {
+ return "Error: format must be specified for dataURLs";
+ }
- List<String> files = isDataURL ? Arrays.asList(fileString) : breakFileString(fileString);
- List<String> indexFiles = isDataURL ? null : breakFileString(indexString);
- List<String> coverageFiles = breakFileString(coverageString);
- List<String> names = breakFileString(nameString);
- List<String> formats = breakFileString(formatString);
- if (names != null && names.size() != files.size()) {
- return "Error: If file is a comma-separated list, names must also be a comma-separated list of the same length";
- }
- if (indexFiles != null && indexFiles.size() != files.size()) {
- return "Error: If file is a comma-separated list, index must also be a comma-separated list of the same length";
- }
- if (isDataURL && formatString == null) {
- return "Error: format must be specified for dataURLs";
- }
+ // Fix formats -- backward compatibility
+ if (formats != null) {
+ for (int i = 0; i < formats.size(); i++) {
+ String formatOrExt = decodeFileString(formats.get(i));
+ String format = formatOrExt.startsWith(".") ? formatOrExt.substring(1) : formatOrExt;
+ formats.set(i, format);
- // Fix formats -- backward compatibility
- if (formats != null) {
- for (int i = 0; i < formats.size(); i++) {
- String formatOrExt = decodeFileString(formats.get(i));
- String format = formatOrExt.startsWith(".") ? formatOrExt.substring(1) : formatOrExt;
- formats.set(i, format);
+ }
+ }
+ List<ResourceLocator> fileLocators = new ArrayList<>();
+
+ if (!SessionReader.isSessionFile(fileString) && merge == false) {
+ igv.newSession();
}
- }
- List<ResourceLocator> fileLocators = new ArrayList<>();
+ // Create set of loaded files
+ Set<String> loadedFiles = new HashSet<>();
+ for (ResourceLocator rl : igv.getDataResourceLocators()) {
+ loadedFiles.add(rl.getPath());
+ }
- if (!SessionReader.isSessionFile(fileString) && merge == false) {
- igv.newSession();
- }
- // Create set of loaded files
- Set<String> loadedFiles = new HashSet<>();
- for (ResourceLocator rl : igv.getDataResourceLocators()) {
- loadedFiles.add(rl.getPath());
- }
+ // Loop through files
+ for (int fi = 0; fi < files.size(); fi++) {
+ String f = resolveFileReference(files.get(fi));
- // Loop through files
- for (int fi = 0; fi < files.size(); fi++) {
- String f = files.get(fi);
- if (!FileUtils.isRemote(f)) {
- File maybeFile = getFile(f);
- if (maybeFile.exists()) {
- f = maybeFile.getAbsolutePath();
- } else {
- maybeFile = new File(this.scriptDir, StringUtils.stripQuotes(f));
- if (maybeFile.exists()) {
- f = maybeFile.getAbsolutePath();
- }
+ if (isDataURL && formats == null) {
+ return "Error: format must be specified for dataURLs";
}
- }
- if (isDataURL && formats == null) {
- return "Error: format must be specified for dataURLs";
- }
+ // Skip already loaded files
+ if (!dup && loadedFiles.contains(f)) continue;
- // Skip already loaded files
- if (!dup && loadedFiles.contains(f)) continue;
-
- if (SessionReader.isSessionFile(f)) {
- igv.loadSession(f, locus);
- } else {
+ if (SessionReader.isSessionFile(f)) {
+ igv.loadSession(f, locus);
+ } else {
- ResourceLocator rl = new ResourceLocator(f);
+ ResourceLocator rl = new ResourceLocator(f);
- if (names != null) {
- rl.setName(names.get(fi));
- } else if (isDataURL) {
- rl.setName("Data");
- }
- if (indexFiles != null) {
- rl.setIndexPath(indexFiles.get(fi));
- }
- if (coverageFiles != null) {
- rl.setCoverage(coverageFiles.get(fi));
- }
- if (formats != null) {
- rl.setFormat(formats.get(fi));
- }
+ if (names != null) {
+ rl.setName(names.get(fi));
+ } else if (isDataURL) {
+ rl.setName("Data");
+ }
+ if (indexFiles != null) {
+ rl.setIndexPath(indexFiles.get(fi));
+ }
+ if (coverageFiles != null) {
+ rl.setCoverage(coverageFiles.get(fi));
+ }
+ if (formats != null) {
+ rl.setFormat(formats.get(fi));
+ }
- if (params != null) {
- String trackLine = createTrackLine(params);
- rl.setTrackLine(trackLine);
- }
+ if (params != null) {
+ String trackLine = createTrackLine(params);
+ rl.setTrackLine(trackLine);
+ }
- if (!isDataURL && rl.isLocal()) {
- File file = new File(rl.getPath());
- if (!file.exists()) {
- return "Error: " + f + " does not exist.";
+ if (!isDataURL && rl.isLocal()) {
+ File file = new File(rl.getPath());
+ if (!file.exists()) {
+ return "Error: " + f + " does not exist.";
+ }
}
+ fileLocators.add(rl);
}
- fileLocators.add(rl);
}
- }
- if (fileLocators.size() > 0) {
- igv.loadTracks(fileLocators);
- }
+ if (fileLocators.size() > 0) {
+ igv.loadTracks(fileLocators);
+ }
- if (locus != null && !locus.equals("null")) {
- igv.goToLocus(locus);
- //If locus is a single base, we sort by base
- String[] tokens = locus.split(":", 2);
- if (tokens.length == 2) {
- try {
- int pos = Integer.parseInt(tokens[1].replace(",", ""));
- if (pos >= 0 && sort == null) sort = "base";
- } catch (Exception e) {
- //pass
+
+ if (locus != null) {
+ igv.goToLocus(locus);
+ }
+
+ // Sort alignment tracks
+ if (igv.getAlignmentTracks().size() > 0) {
+
+ //If locus is a single base, and session has alignment tracks, provide default sort option (base)
+ if (locus != null && sort == null) {
+ String[] tokens = locus.split(":", 2);
+ if (tokens.length == 2 && !tokens[1].contains("-")) {
+ // Sort by base by default
+ sort = "base";
+ }
+ }
+
+ if (sort != null) {
+ final SortOption sortOption = getAlignmentSortOption(sort);
+ igv.sortAlignmentTracks(sortOption, sortTag, false);
}
}
- }
- if (sort != null) {
- final SortOption sortOption = getAlignmentSortOption(sort);
- igv.sortAlignmentTracks(sortOption, sortTag, false);
+ return CommandListener.OK;
+ } finally {
+ Globals.setBatch(currentBatchSetting);
}
+ }
- return CommandListener.OK;
+ private String resolveFileReference(String f) {
+
+ if (FileUtils.isRemote(f)) {
+ return f;
+ } else {
+ File maybeFile = getFile(f);
+ if (maybeFile.exists()) {
+ f = maybeFile.getAbsolutePath();
+ }
+ return f;
+ }
}
@@ -956,6 +959,7 @@ public class CommandExecutor {
* @return
*/
private File getFile(String path) {
+
// Strip trailing & leading quotes
path = StringUtils.stripQuotes(path);
@@ -1050,11 +1054,11 @@ public class CommandExecutor {
reverseString = param4;
} else {
locusString = param2;
- reverseString = param3;
+ reverseString = param3;
}
// Special case, "reverse" is a resered word for inverting sorting. Locus is optional
- if(reverseString == null && "reverse".equalsIgnoreCase(locusString)) {
+ if (reverseString == null && "reverse".equalsIgnoreCase(locusString)) {
reverseString = locusString;
locusString = null;
}
=====================================
src/main/java/org/broad/igv/batch/CommandListener.java
=====================================
@@ -35,6 +35,7 @@ import org.broad.igv.oauth.OAuthUtils;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.ui.IGV;
+import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.StringUtils;
@@ -224,15 +225,20 @@ public class CommandListener implements Runnable {
if (command.equals("/oauthCallback")) {
OAuthProvider provider = OAuthUtils.getInstance().getProviderForState(params.get("state"));
-
- if (params.containsKey("code")) {
+ if (params.containsKey("error")) {
+ sendTextResponse(out, "Error authorizing IGV: " + params.get("error"));
+ } else if (params.containsKey("code")) {
provider.setAuthorizationCode(params.get("code"));
+ sendTextResponse(out, "Authorization successful. You may close this tab.");
} else if (params.containsKey("token")) {
// Very doubtful this is ever called -- its not a normal OAuth flow
log.info("Oauth token received");
provider.setAccessToken(params.get("token"));
+ sendTextResponse(out, "Authorization successful. You may close this tab.");
+ } else {
+ sendTextResponse(out, "Unsuccessful authorization response: " + inputLine);
}
- sendTextResponse(out, "Authorization successful. You may close this tab.");
+
if (PreferencesManager.getPreferences().getAsBoolean(Constants.PORT_ENABLED) == false) {
// Turn off port
@@ -389,8 +395,11 @@ public class CommandListener implements Runnable {
// Default for merge is "false" for session files, "true" otherwise
boolean merge;
if (mergeValue != null) {
- // Explicit setting
- merge = mergeValue.equalsIgnoreCase("true");
+ if ("ask".equals(mergeValue)) {
+ merge = !MessageUtils.confirm("Unload current session before loading new tracks?");
+ } else {
+ merge = mergeValue.equalsIgnoreCase("true");
+ }
} else if (file.endsWith(".xml") || file.endsWith(".php") || file.endsWith(".php3")) {
// Session file
merge = false;
=====================================
src/main/java/org/broad/igv/feature/genome/Genome.java
=====================================
@@ -383,7 +383,7 @@ public class Genome {
}
public String getBlatDB() {
- return blatDB != null ? blatDB : id;
+ return blatDB;
}
public void setBlatDB(String blatDB) {
=====================================
src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
=====================================
@@ -171,14 +171,18 @@ public class JsonGenomeLoader extends GenomeLoader {
}
}
- JsonElement ucscIDElement = json.get("ucscID");
- if (ucscIDElement != null) {
- newGenome.setUcscID(ucscIDElement.getAsString());
- }
JsonElement blatDB = json.get("blatDB");
if (blatDB != null) {
newGenome.setUcscID(blatDB.getAsString());
}
+ JsonElement ucscIDElement = json.get("ucscID");
+ if (ucscIDElement != null) {
+ newGenome.setUcscID(ucscIDElement.getAsString());
+ if(blatDB == null) {
+ newGenome.setBlatDB(ucscIDElement.getAsString());
+ }
+ }
+
JsonElement aliasURL = json.get("aliasURL");
if (aliasURL != null) {
String aliasPath = FileUtils.getAbsolutePath(aliasURL.getAsString(), genomePath);
=====================================
src/main/java/org/broad/igv/feature/tribble/MUTCodec.java
=====================================
@@ -34,6 +34,8 @@ import org.broad.igv.Globals;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.feature.Mutation;
import org.broad.igv.feature.genome.Genome;
+import org.broad.igv.prefs.PreferencesManager;
+import org.broad.igv.track.TrackProperties;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
@@ -45,6 +47,8 @@ import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.Map;
+import static org.broad.igv.prefs.Constants.MUT_COORDS;
+
/**
* Codec for .mut and .maf mutation files
*
@@ -70,6 +74,7 @@ public class MUTCodec extends AsciiFeatureCodec<Mutation> {
private int tumorAllele1Column = -1;
private int tumorAllele2Column = -1;
private int errorCount = 0;
+ private TrackProperties.BaseCoord coords = TrackProperties.BaseCoord.ZERO;
public MUTCodec(String path, Genome genome) {
@@ -92,10 +97,10 @@ public class MUTCodec extends AsciiFeatureCodec<Mutation> {
}
public Void readActualHeader(LineIterator reader) {
- String nextLine = null;
+ TrackProperties.BaseCoord coordsValue = null;
while (reader.hasNext()) {
- nextLine = reader.peek();
+ String nextLine = reader.peek();
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#samples")) {
String[] tokens = Globals.whitespacePattern.split(nextLine, 2);
@@ -107,11 +112,33 @@ public class MUTCodec extends AsciiFeatureCodec<Mutation> {
samples[i] = samples[i].trim();
}
}
+ } else if (nextLine.startsWith("#coords")) {
+ String[] tokens = Globals.equalPattern.split(nextLine);
+ if(tokens.length > 1) {
+ String value = tokens[1].trim();
+ if (value.equals("0")) {
+ coordsValue = TrackProperties.BaseCoord.ZERO;
+ } else if (value.equals("1")) {
+ coordsValue = TrackProperties.BaseCoord.ONE;
+ } else {
+ log.error("Unknown #coords value: " + value + " Legal values are 0 and 1");
+ }
+ } else {
+ log.error("#coords directive must have value, e.g. #coords=1");
+ }
}
reader.next();
continue;
}
+ // If coords are explicitly set use setting, otherwise check preferences
+ if(coordsValue != null) {
+ this.coords = coordsValue;
+ } else {
+ this.coords = "1".equals(PreferencesManager.getPreferences().get(MUT_COORDS, "0")) ?
+ TrackProperties.BaseCoord.ONE : TrackProperties.BaseCoord.ZERO;
+ }
+
String[] tokens = Globals.tabPattern.split(nextLine);
if (tokens.length >= 5) {
reader.next();
@@ -153,7 +180,7 @@ public class MUTCodec extends AsciiFeatureCodec<Mutation> {
int start;
try {
- start = Integer.parseInt(tokens[startColumn].trim()) - 1;
+ start = Integer.parseInt(tokens[startColumn].trim());
} catch (NumberFormatException e) {
errorCount++;
if (errorCount > 100) {
@@ -177,6 +204,14 @@ public class MUTCodec extends AsciiFeatureCodec<Mutation> {
}
}
+
+ // MAF files use the 1-based inclusive convention for coordinates. The convention is not
+ // specified for MUT files, and it appears both conventions have been used. We can detect
+ // the convention used for single base mutations by testing start == end.
+ if (isMAF || (start == end) || coords == TrackProperties.BaseCoord.ONE) {
+ start--;
+ }
+
String sampleId = "Unknown";
if(sampleColumn >= 0) {
sampleId = tokens[sampleColumn].trim();
@@ -422,6 +457,6 @@ Match_Norm_Seq_Allele2
@Override
public boolean canDecode(String path) {
- return isMutationAnnotationFile(new ResourceLocator(path));
+ return isMutationAnnotationFile(new ResourceLocator(path));
}
}
=====================================
src/main/java/org/broad/igv/oauth/OAuthProvider.java
=====================================
@@ -201,7 +201,7 @@ public class OAuthProvider {
if (clientSecret != null) {
params.put("client_secret", clientSecret);
}
- params.put("redirect_uri", new URLDecoder().decode(redirectURI, "utf-8"));
+ params.put("redirect_uri", URLDecoder.decode(redirectURI, "utf-8"));
params.put("grant_type", "authorization_code");
// set the resource if it necessary for the auth provider dwm08
=====================================
src/main/java/org/broad/igv/prefs/Constants.java
=====================================
@@ -213,6 +213,8 @@ final public class Constants {
public static final String OVERLAY_MUTATIONS_WHOLE_GENOME = "OVERLAY_MUTATIONS_WHOLE_GENOME";
public static final String COLOR_MUTATIONS = "COVER_OVERLAY_KEY";
+ public static final String MUT_COORDS = "MUT_COORDS";
+
// GWAS track options
public static final String GWAS_TRACK_HEIGHT = "GWAS_TRACK_HEIGHT";
public static final String GWAS_DESCRIPTION_CACHE_SIZE = "GWAS_DESCRIPTION_CACHE_SIZE";
=====================================
src/main/java/org/broad/igv/prefs/PreferencesManager.java
=====================================
@@ -24,7 +24,7 @@ public class PreferencesManager implements IGVEventObserver {
private static List<PreferenceGroup> preferenceGroupList;
private static Logger log = LogManager.getLogger(PreferencesManager.class);
private static Map<String, IGVPreferences> preferencesMap = Collections.synchronizedMap(new HashMap<>());
- private static IGVPreferences genericDefaults;
+ private static Map<String, String> genericDefaults;
private static String prefFile; // User preferences file
@@ -79,15 +79,14 @@ public class PreferencesManager implements IGVEventObserver {
}
}
- genericDefaults = new IGVPreferences(defaultPreferences.get(NULL_CATEGORY), null, null);
- Map<String, String> defaults = defaultPreferences.get(NULL_CATEGORY);
+ genericDefaults = defaultPreferences.get(NULL_CATEGORY);
Map<String, String> rnaDefaults = defaultPreferences.get(RNA);
Map<String, String> thirdGenDefaults = defaultPreferences.get(THIRD_GEN);
Map<String, Map<String, String>> userPrefs = loadUserPreferences();
- final IGVPreferences nullPrefs = new IGVPreferences(userPrefs.get(NULL_CATEGORY), defaults, null);
+ final IGVPreferences nullPrefs = new IGVPreferences(userPrefs.get(NULL_CATEGORY), genericDefaults, null);
extractMutationColors(nullPrefs);
preferencesMap.put(NULL_CATEGORY, nullPrefs);
preferencesMap.put(RNA, new IGVPreferences(userPrefs.get(RNA), rnaDefaults, nullPrefs));
@@ -116,6 +115,9 @@ public class PreferencesManager implements IGVEventObserver {
}
}
+ public static String getDefault(String key) {
+ return genericDefaults.get(key);
+ }
public static IGVPreferences getPreferences() {
return getPreferences(NULL_CATEGORY);
}
=====================================
src/main/java/org/broad/igv/sam/AlignmentTrack.java
=====================================
@@ -796,7 +796,11 @@ public class AlignmentTrack extends AbstractTrack implements IGVEventObserver {
for (ReferenceFrame frame : frames) {
final double actloc = location != null ? location : frame.getCenter();
final AlignmentInterval interval = getDataManager().getLoadedInterval(frame);
- interval.sortRows(option, actloc, tag, invertSort);
+ if(interval != null) {
+ interval.sortRows(option, actloc, tag, invertSort);
+ } else {
+ log.warn("Attempt to sort alignments prior to loading");
+ }
}
}
=====================================
src/main/java/org/broad/igv/track/BlatTrack.java
=====================================
@@ -125,6 +125,9 @@ public class BlatTrack extends FeatureTrack {
String db = element.getAttribute("db");
if (db == null || db.length() == 0) {
db = GenomeManager.getInstance().getCurrentGenome().getBlatDB();
+ if(db == null) {
+ db = GenomeManager.getInstance().getCurrentGenome().getId();
+ }
}
try {
this.features = BlatClient.blat(db, sequence);
=====================================
src/main/java/org/broad/igv/track/TrackLoader.java
=====================================
@@ -938,7 +938,7 @@ public class TrackLoader {
String path = locator.getPath();
boolean bypassFileAutoDiscovery =
PreferencesManager.getPreferences().getAsBoolean(BYPASS_FILE_AUTO_DISCOVERY) ||
- GoogleUtils.isGoogleCloud(locator.getPath()) ||
+ GoogleUtils.isGoogleURL(locator.getPath()) ||
path.contains("dropbox.com") ||
path.contains("dataformat=.bam") ||
path.contains("/query.cgi?");
=====================================
src/main/java/org/broad/igv/ui/IGV.java
=====================================
@@ -1539,15 +1539,15 @@ public class IGV implements IGVEventObserver {
}
public List<FeatureTrack> getFeatureTracks() {
- Iterable<FeatureTrack> featureTracksIter = Iterables.filter(getAllTracks(), FeatureTrack.class);
- List<FeatureTrack> featureTracks = Lists.newArrayList(featureTracksIter);
- return featureTracks;
+ return Lists.newArrayList(Iterables.filter(getAllTracks(), FeatureTrack.class));
}
public List<DataTrack> getDataTracks() {
- Iterable<DataTrack> dataTracksIter = Iterables.filter(getAllTracks(), DataTrack.class);
- List<DataTrack> dataTracks = Lists.newArrayList(dataTracksIter);
- return dataTracks;
+ return Lists.newArrayList(Iterables.filter(getAllTracks(), DataTrack.class));
+ }
+
+ public List<AlignmentTrack> getAlignmentTracks() {
+ return Lists.newArrayList(Iterables.filter(getAllTracks(), AlignmentTrack.class));
}
public void clearSelections() {
=====================================
src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java
=====================================
@@ -109,7 +109,7 @@ public class LoadFromURLMenuAction extends MenuAction {
if (dlg.getIndexURL() != null) {
String indexUrl = dlg.getIndexURL().trim();
- if (GoogleUtils.isGoogleCloud(indexUrl) || GoogleUtils.isGoogleDrive(indexUrl)) {
+ if (GoogleUtils.isGoogleURL(indexUrl)) {
enableGoogleMenu();
}
@@ -151,7 +151,7 @@ public class LoadFromURLMenuAction extends MenuAction {
private String mapURL(String url) {
url = url.trim();
- if (GoogleUtils.isGoogleCloud(url) || GoogleUtils.isGoogleDrive(url)) {
+ if (GoogleUtils.isGoogleURL(url)) {
enableGoogleMenu();
}
=====================================
src/main/java/org/broad/igv/ui/color/ColorUtilities.java
=====================================
@@ -201,6 +201,10 @@ public class ColorUtilities {
Color c = null;
if (string.contains(",")) {
+ if(string.startsWith("rgb(") && string.endsWith(")")) {
+ // javascript style string
+ string = string.substring(4, string.length() - 1);
+ }
if (string.contains(".")) {
String[] rgb = string.split(",");
int red = (int) (255 * Double.parseDouble(rgb[0]));
=====================================
src/main/java/org/broad/igv/util/GoogleUtils.java
=====================================
@@ -29,12 +29,9 @@ public class GoogleUtils {
public static final String GOOGLE_DRIVE_HOST = "drive.google.com";
public static boolean isGoogleURL(String url) {
- return url != null && (isGoogleCloud(url) || isGoogleDrive(url) || isGoogleStorageURL(url));
+ return url != null && (isGoogleDrive(url) || isGoogleStorageURL(url));
}
- public static boolean isGoogleCloud(String url) {
- return url != null && (url.startsWith("gs://") || url.contains(GOOGLE_API_HOST));
- }
public static boolean isGoogleDrive(String url) {
return url != null && (url.contains(GOOGLE_DRIVE_HOST) || url.contains("www.googleapis.com/drive"));
=====================================
src/main/java/org/broad/igv/util/HttpUtils.java
=====================================
@@ -203,7 +203,7 @@ public class HttpUtils {
urlString = GoogleUtils.translateGoogleCloudURL(urlString);
}
- if (GoogleUtils.isGoogleCloud(urlString)) {
+ if (GoogleUtils.isGoogleURL(urlString)) {
if (urlString.indexOf("alt=media") < 0) {
urlString = URLUtils.addParameter(urlString, "alt=media");
}
@@ -679,12 +679,14 @@ public class HttpUtils {
// If the URL is protected via an oAuth provider fetch token, and optionally map url with find/replace string.
OAuthProvider oauthProvider = OAuthUtils.getInstance().getProviderForURL(url);
+
if (oauthProvider != null) {
//Google is skipped here as we don't yet know if the url is protected or not. Login is invoked after 401 error
if(!oauthProvider.isGoogle()) {
oauthProvider.checkLogin();
}
token = oauthProvider.getAccessToken();
+
if (oauthProvider.findString != null) {
// A hack, supported for backward compatibility but not reccomended
url = HttpUtils.createURL(url.toExternalForm().replaceFirst(oauthProvider.findString, oauthProvider.replaceString));
@@ -720,6 +722,7 @@ public class HttpUtils {
GoogleUtils.getProjectID() != null &&
GoogleUtils.getProjectID().length() > 0 &&
!hasQueryParameter(url, "userProject")) {
+
url = addQueryParameter(url, "userProject", GoogleUtils.getProjectID());
}
@@ -860,7 +863,7 @@ public class HttpUtils {
message = conn.getResponseMessage();
String details = readErrorStream(conn);
- if (url.getHost().equals("www.googleapis.com") && details.contains("requester pays bucket")) {
+ if (GoogleUtils.isGoogleURL(url.toExternalForm()) && details.contains("requester pays bucket")) {
MessageUtils.showMessage("<html>" + details + "<br>Use Google menu to set project.");
}
=====================================
src/main/java/org/broad/igv/util/blat/BlatClient.java
=====================================
@@ -43,9 +43,7 @@ import org.broad.igv.util.*;
import java.io.IOException;
import java.net.URL;
import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
+import java.util.*;
/**
* Port of perl script blatPlot.pl http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts
@@ -63,10 +61,12 @@ public class BlatClient {
public static List<PSLRecord> blat(String db, String userSeq) throws IOException {
String serverType = PreferencesManager.getPreferences().get(Constants.BLAT_SERVER_TYPE, "");
- String urlpref = PreferencesManager.getPreferences().get(
- Constants.BLAT_URL,
- "https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=$SEQUENCE&type=DNA&db=$DB&output=json")
- .trim();
+ String urlpref = PreferencesManager.getPreferences().get(Constants.BLAT_URL);
+ if (urlpref == null || urlpref.trim().length() == 0) {
+ MessageUtils.showMessage("BLAT url is not configured");
+ return Collections.EMPTY_LIST;
+ }
+ urlpref = urlpref.trim();
if (serverType.equalsIgnoreCase("web_blat") || !urlpref.contains("$SEQUENCE")) {
return LegacyBlatClient.blat(userSeq);
@@ -140,8 +140,16 @@ public class BlatClient {
public static void doBlatQuery(final String userSeq, final String trackLabel) {
try {
- Genome genome = IGV.hasInstance() ? GenomeManager.getInstance().getCurrentGenome() : null;
- String db = genome == null ? "hg19" : genome.getBlatDB();
+ Genome genome = GenomeManager.getInstance().getCurrentGenome();
+ String db = genome.getBlatDB();
+ if (db == null) {
+ // If this is a known UCSC genome, or a custom blat server is configured, use the genome ID
+ if (knownUCSCGenomes.contains(genome.getId()) ||
+ !PreferencesManager.getPreferences().get(Constants.BLAT_URL).equals(PreferencesManager.getDefault(Constants.BLAT_URL))) {
+ db = genome.getId();
+ }
+ }
+
List<PSLRecord> features = blat(db, userSeq);
if (features.isEmpty()) {
MessageUtils.showMessage("No features found");
@@ -177,22 +185,28 @@ public class BlatClient {
doBlatQuery(userSeq, "BLAT");
}
- private static String htmlToString (String str) {
+ private static String htmlToString(String str) {
// Remove script tags
int idx1;
int count = 0;
- while((idx1 = str.indexOf("<script")) >= 0 && count < 10) {
+ while ((idx1 = str.indexOf("<script")) >= 0 && count < 10) {
int idx2 = str.indexOf("</script>", idx1);
- if(idx1 > 0 && idx2 > idx1) {
+ if (idx1 > 0 && idx2 > idx1) {
str = str.substring(0, idx1) + str.substring(idx2 + 9);
}
count++;
}
- str = str.replaceAll("\\<.*?>","").replace('\n', ' ');
+ str = str.replaceAll("\\<.*?>", "").replace('\n', ' ');
return str;
}
+ static Set knownUCSCGenomes = new HashSet<>(Arrays.asList("hg18", "hg19", "hg38", "ce10", "ce11", "galGal4",
+ "galGal5", "galGal6", "panTro3", "panTro4", "panTro5", "panTro6", "felCat6", "bosTau7", "bosTau8",
+ "bosTau9", "dm3", "dm6", "canFam3", "canFam5", "mm8", "mm9", "mm10", "mm39", "rn5", "rn6", "rn7",
+ "rheMac3", "rheMac8", "rheMac10", "sacCer3", "susScr3", "xenTro9", "danRer10", "danRer11",
+ "gorGor4", "gorGor6", "panPan2", "susScr11", "strPur2"));
+
}
=====================================
src/main/java/org/broad/igv/variant/VariantTrack.java
=====================================
@@ -236,8 +236,17 @@ public class VariantTrack extends FeatureTrack implements IGVEventObserver {
boolean bypassFileAutoDiscovery = prefMgr.getAsBoolean(BYPASS_FILE_AUTO_DISCOVERY);
if (vcfToBamMapping == null && path != null && !bypassFileAutoDiscovery) {
- if (ParsingUtils.fileExists(path + ".mapping")) {
- vcfToBamMapping = path + ".mapping";
+ String mappingFile = "";
+ int queryStart = path.indexOf("?");
+ if (queryStart > -1)
+ {
+ String query = path.substring(queryStart);
+ path = path.substring(0,queryStart);
+ mappingFile = path + ".mapping" + query;
+ }
+
+ if (ParsingUtils.fileExists(mappingFile)) {
+ vcfToBamMapping = mappingFile;
}
}
=====================================
src/main/resources/org/broad/igv/prefs/preferences.tab
=====================================
@@ -55,6 +55,8 @@ MUTATION_Non-coding_Transcript_COLOR Non-coding Transcript color 0,0,150
MUTATION_Other_AA_changing_COLOR Other AA Changing color 0,150,150
MUTATION_Other_likely_neutral_COLOR Other Likely Neutral color 225,180,225
MUTATION_UNKNOWN_COLOR_KEY Unknown color 0,180,225
+##Coordinate System
+MUT_COORDS Mut file coordinate convention. 0 = zero based half-open, 1 = one based fully closed. select 0|1 0
#Charts
CHART.DRAW_TOP_BORDER Draw top border boolean FALSE
=====================================
src/test/java/org/broad/igv/ui/color/ColorUtilitiesTest.java
=====================================
@@ -54,4 +54,12 @@ public class ColorUtilitiesTest {
Color c = ColorUtilities.stringToColor("#AAAAAA");
assertEquals(grey, c);
}
+
+ @Test
+ public void testRGBToColor() throws Exception {
+ // Test parsing javascript style rgb string
+ String rgbString = "rgb(0,0,255)";
+ Color b = ColorUtilities.stringToColor(rgbString);
+ assertEquals(Color.blue, b);
+ }
}
=====================================
test/batch/exit.txt deleted
=====================================
@@ -1,2 +0,0 @@
-# Should cause IGV to close
-exit
=====================================
test/batch/multiple_bams.txt
=====================================
@@ -5,12 +5,12 @@ load gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam
load gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam
load gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam
load gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam
-#snapshot
+snapshot
goto myc muc1
-#snapshot myc_myc1.png
-# goto tp53
-# zoomin
-# zoomin
-# zoomin
-# squish
-#snapshot tp53_squished.png
+snapshot myc_myc1.png
+goto tp53
+zoomin
+zoomin
+zoomin
+squish
+snapshot tp53_squished.png
=====================================
test/batch/path_with_spaces.txt
=====================================
@@ -22,3 +22,7 @@ goto chr1:16270500-16270600
load "../data/folder with spaces/test+wp.wig"
snapshot "test+wp.png"
+# Test genome in quoted string
+genome "../data/genomes/hg18.unittest.genome"
+
+
=====================================
test/data/mut/tcga_20080711_phase1_filtered_nonsilent.mut
=====================================
@@ -0,0 +1,455 @@
+#coords=1
+chr start end patient type gene phase center shared strand site supertype context class newbase status validation call evidence filtered use hypermutated
+1 2072180 2072180 TCGA-06-0206 Missense PRKCZ 1 BCM No + PRKCZ|chr1:2072180-2072180 Missense cgggcGcggga G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+1 2106249 2106249 TCGA-02-0083 Missense PRKCZ 1 BCM No + PRKCZ|chr1:2106249-2106249 Missense agtcaGagttc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 6112865 6112865 TCGA-06-0189 Missense CHD5 1 genome.wustl.edu No - CHD5|chr1:6112865-6112865 Missense acccgCacaat C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+1 11224264 11224264 TCGA-02-0083 Missense FRAP1 1 genome.wustl.edu No - FRAP1|chr1:11224264-11224264 Missense ctcgaGcaatg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 12175619 12175619 TCGA-06-0126 Missense TNFRSF1B 1 genome.wustl.edu No + TNFRSF1B|chr1:12175619-12175619 Missense tgtccAcacga A C Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+1 15717209 15717209 TCGA-02-0083 Missense CASP9 1 BCM No - CASP9|chr1:15717209-15717209 Missense ttctgGaggat G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 16347951 16347951 TCGA-02-0114 Missense EPHA2 1 BCM No - EPHA2|chr1:16347951-16347951 Missense tggtgGcgcca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 23758222 23758222 TCGA-02-0114 Missense ID3 1 broad.mit.edu No - ID3|chr1:23758222-23758222 Missense atggcCcccac C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 27555547 27555547 TCGA-02-0028 Missense MAP3K6 1 broad.mit.edu No - MAP3K6|chr1:27555547-27555547 Missense aacggGagtac G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 114742087 114742087 TCGA-02-0010 Nonsense TRIM33 1 broad.mit.edu No - TRIM33|chr1:114742087-114742087 Nonsense atttgAaggta A T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 115060270 115060270 TCGA-02-0085 Missense NRAS 1 BCM No - NRAS|chr1:115060270-115060270 Missense agcagGtggtg G (other) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+1 149055490 149055490 TCGA-02-0083 Missense ARNT 1 genome.wustl.edu No - ARNT|chr1:149055490-149055490 Missense tagccCctcct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 153299877 153299877 TCGA-02-0083 Missense ADAM15 1 BCM No + ADAM15|chr1:153299877-153299877 Missense atctgGtccct G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 165625522 165625522 TCGA-02-0043 Missense POU2F1 1 BCM No + POU2F1|chr1:165625522-165625522 Missense aaagcGaattg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 195340175 195340175 TCGA-02-0010 Missense ASPM 1 broad.mit.edu No - ASPM|chr1:195340175-195340175 Missense agctgTtataa T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 195365053 195365053 TCGA-02-0010 Missense ASPM 1 broad.mit.edu No - ASPM|chr1:195365053-195365053 Missense ctttgTccaag T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 202010148 202010148 TCGA-02-0114 Missense LAX1 1 genome.wustl.edu No + LAX1|chr1:202010148-202010148 Missense gtggaAgccag A T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 202674772 202674772 TCGA-02-0043 Missense PIK3C2B 1 broad.mit.edu No - PIK3C2B|chr1:202674772-202674772 Missense aggtgGagcat G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 202774027 202774027 TCGA-06-0129 Missense MDM4 1 BCM, broad.mit.edu, genome.wustl.edu Yes + MDM4|chr1:202774027-202774027 Missense gcctaCctcag C (other) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+1 202854501 202854501 TCGA-02-0043 Missense LRRN2 1 BCM No - LRRN2|chr1:202854501-202854501 Missense tccggGagatg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 206025059 206025059 TCGA-02-0010 Missense CD46 1 BCM No + CD46|chr1:206025059-206025059 Missense ctgtgAttgtt A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 212237253 212237253 TCGA-02-0010 Missense PROX1 1 broad.mit.edu No + PROX1|chr1:212237253-212237253 Missense gctgcGccagc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+1 212853776 212853776 TCGA-02-0055 Missense CENPF 1 genome.wustl.edu No + CENPF|chr1:212853776-212853776 Missense tcagaAaattc A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+1 212888794 212888794 TCGA-02-0099 Splice_site CENPF 1 genome.wustl.edu No + CENPF|chr1:212888794-212888794 Other gcaaaGtaagt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 5751538 5751538 TCGA-06-0173 Nonsense SOX11 1 broad.mit.edu No + SOX11|chr2:5751538-5751538 Nonsense acttcGagttc G (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 5751587 5751587 TCGA-02-0010 Missense SOX11 1 broad.mit.edu No + SOX11|chr2:5751587-5751587 Missense gggggActggc A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 15999768 15999768 TCGA-02-0028 Missense MYCN 1 broad.mit.edu No + MYCN|chr2:15999768-15999768 Missense gacccCcccgg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 47484039 47484039 TCGA-02-0075 Missense MSH2 1 genome.wustl.edu No + MSH2|chr2:47484039-47484039 Missense tggggCcggca C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 47557079 47557079 TCGA-02-0083 Missense MSH2 1 genome.wustl.edu No + MSH2|chr2:47557079-47557079 Missense aattgGgtgtt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 47880076 47880076 TCGA-02-0114 Missense MSH6 1 BCM No + MSH6|chr2:47880076-47880076 Missense gagtgGaacag G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 47881696 47881696 TCGA-02-0010 Missense MSH6 1 BCM No + MSH6|chr2:47881696-47881696 Missense aagaaCggagg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 47881792 47881792 TCGA-02-0083 Missense MSH6 1 BCM No + MSH6|chr2:47881792-47881792 Missense tcgcaGtgttg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 47886856 47886856 TCGA-02-0043 Missense MSH6 1 BCM No + MSH6|chr2:47886856-47886856 Missense aggtaCtgcaa C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 60541333 60541333 TCGA-06-0176 Missense BCL11A 1 broad.mit.edu No - BCL11A|chr2:60541333-60541333 Missense gcagaCgcagc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 60542011 60542011 TCGA-06-0133 Missense BCL11A 1 broad.mit.edu No - BCL11A|chr2:60542011-60542011 Missense actacGgcttc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 60542638 60542638 TCGA-02-0083 Missense BCL11A 1 broad.mit.edu No - BCL11A|chr2:60542638-60542638 Missense tgaatCcaatg C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 60542986 60542986 TCGA-02-0028 Missense BCL11A 1 broad.mit.edu No - BCL11A|chr2:60542986-60542986 Missense aacacGcacag G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 102332064 102332064 TCGA-02-0007 Missense IL1RL1 1 BCM No + IL1RL1|chr2:102332064-102332064 Missense ccagaTtctgc T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 127170093 127170093 TCGA-02-0114 Missense GYPC 1 genome.wustl.edu No + GYPC|chr2:127170093-127170093 Missense ccaagGgcacg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 189576409 189576409 TCGA-02-0043 Missense COL3A1 1 broad.mit.edu No + COL3A1|chr2:189576409-189576409 Missense tcaaaGgtgaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 189576733 189576733 TCGA-02-0083 Missense COL3A1 1 broad.mit.edu No + COL3A1|chr2:189576733-189576733 Missense tcgtgGtcttc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 191571219 191571219 TCGA-06-0185 Missense STAT1 1 BCM No - STAT1|chr2:191571219-191571219 Missense caagaAgatgt A T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 215948361 215948361 TCGA-02-0083 Missense FN1 1 broad.mit.edu No - FN1|chr2:215948361-215948361 Missense ttcagCcattg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 215948606 215948606 TCGA-02-0010 Missense FN1 1 broad.mit.edu No - FN1|chr2:215948606-215948606 Missense tcgacGcctcc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 215997243 215997243 TCGA-02-0114 Missense FN1 1 broad.mit.edu No - FN1|chr2:215997243-215997243 Missense tcttaCcattc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 215998200 215998200 TCGA-02-0114 Missense FN1 1 broad.mit.edu No - FN1|chr2:215998200-215998200 Missense ctcacCcccag C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 219249113 219249113 TCGA-02-0014 Nonsense STK36 1 genome.wustl.edu No + STK36|chr2:219249113-219249113 Nonsense ctctgGtctgt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 222055639 222055639 TCGA-02-0083 Missense EPHA4 1 genome.wustl.edu No - EPHA4|chr2:222055639-222055639 Missense tgctcCcctga C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 227368280 227368280 TCGA-02-0010 Missense IRS1 1 genome.wustl.edu No - IRS1|chr2:227368280-227368280 Missense gaaacGccaca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 227370416 227370416 TCGA-02-0033 Missense IRS1 1 genome.wustl.edu No - IRS1|chr2:227370416-227370416 Missense ctcctCggatg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+2 233961724 233961724 TCGA-02-0114 Missense DGKD 1 broad.mit.edu No + DGKD|chr2:233961724-233961724 Missense agggcGaacgc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+2 240599706 240599706 TCGA-02-0099 Splice_site NDUFA10 1 genome.wustl.edu No - NDUFA10|chr2:240599706-240599706 Other atgagGtgagc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 366197 366197 TCGA-02-0114 Missense CHL1 1 broad.mit.edu No + CHL1|chr3:366197-366197 Missense aacagCcactc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 27208682 27208682 TCGA-02-0010 Missense NEK10 1 genome.wustl.edu No - NEK10|chr3:27208682-27208682 Missense cgatgAtatca A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 30666785 30666785 TCGA-02-0014 Missense TGFBR2 1 broad.mit.edu No + TGFBR2|chr3:30666785-30666785 Missense agaacAtaaca A T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 37017543 37017543 TCGA-02-0083 Missense MLH1 1 genome.wustl.edu No + MLH1|chr3:37017543-37017543 Missense ttcgaGgtgag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 37042321 37042321 TCGA-02-0083 Missense MLH1 1 genome.wustl.edu No + MLH1|chr3:37042321-37042321 Missense cccagGccatt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 37056750 37056750 TCGA-02-0014 Missense MLH1 1 genome.wustl.edu No + MLH1|chr3:37056750-37056750 Missense acagcAtcaaa A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 41240577 41240577 TCGA-02-0028 Splice_site CTNNB1 1 genome.wustl.edu No + CTNNB1|chr3:41240577-41240577 Other tcaagGtttgt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 46454625 46454625 TCGA-02-0114 Splice_site LTF 1 genome.wustl.edu No - LTF|chr3:46454625-46454625 Other tcgcaGgctaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 46471868 46471868 TCGA-02-0010 Missense LTF 1 genome.wustl.edu No - LTF|chr3:46471868-46471868 Missense tgtgtCgcctg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 50288996 50288996 TCGA-02-0083 Missense SEMA3B 1 genome.wustl.edu No + SEMA3B|chr3:50288996-50288996 Missense aggtgGcagcg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 53188716 53188716 TCGA-06-0145 Missense PRKCD 1 BCM No + PRKCD|chr3:53188716-53188716 Missense aggggCgcgtc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 129846483 129846483 TCGA-02-0099 Missense RPN1 1 genome.wustl.edu No - RPN1|chr3:129846483-129846483 Missense atttgGaagta G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 143659194 143659194 TCGA-02-0010 Nonsense ATR 1 broad.mit.edu No - ATR|chr3:143659194-143659194 Nonsense tttttCgaaga C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 172205794 172205794 TCGA-02-0014 Missense SLC2A2 1 broad.mit.edu No - SLC2A2|chr3:172205794-172205794 Missense atgtgGctcag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 180399335 180399355 TCGA-06-0166 Inframe_Del PIK3CA 1 BCM No + PIK3CA|chr3:180399335-180399355 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 180399357 180399359 TCGA-02-0046 Inframe_Del PIK3CA 1 BCM No + PIK3CA|chr3:180399357-180399359 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 180399570 180399570 TCGA-02-0116 Missense PIK3CA 1 BCM No + PIK3CA|chr3:180399570-180399570 Missense aagacGacttt G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 180404247 180404247 TCGA-02-0047 Missense PIK3CA 1 BCM No + PIK3CA|chr3:180404247-180404247 Missense gtgaaTgtaaa T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 180410674 180410674 TCGA-02-0037 Missense PIK3CA 1 BCM No + PIK3CA|chr3:180410674-180410674 Missense aacacTgtcca T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 180434766 180434766 TCGA-06-0171 Missense PIK3CA 1 BCM, hgsc.bcm.edu No + PIK3CA|chr3:180434766-180434766 Missense aacaaAtgaat A G Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+3 187469360 187469361 TCGA-02-0054 Frameshift_Ins DGKG 1 BCM No - DGKG|chr3:187469360-187469361 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 197096286 197096286 TCGA-02-0043 Nonsense TNK2 1 broad.mit.edu No - TNK2|chr3:197096286-197096286 Nonsense gaaagCgactg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+3 197098255 197098255 TCGA-06-0189 Nonsense TNK2 1 broad.mit.edu No - TNK2|chr3:197098255-197098255 Nonsense gtcgtGgatga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+3 197106537 197106537 TCGA-02-0014 Missense TNK2 1 broad.mit.edu No - TNK2|chr3:197106537-197106537 Missense gcctgGctggg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+4 8633952 8633952 TCGA-02-0009 Missense GPR78 1 genome.wustl.edu No + GPR78|chr4:8633952-8633952 Missense gctacGccgga G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+4 54828591 54828591 TCGA-06-0174 Missense PDGFRA 1 BCM, genome.wustl.edu Yes + PDGFRA|chr4:54828591-54828591 Missense tcctgGctgaa G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+4 55288766 55288766 TCGA-02-0083 Missense KIT 1 BCM, broad.mit.edu, genome.wustl.edu Yes + KIT|chr4:55288766-55288766 Missense ctggaGctttc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+4 153463593 153463593 TCGA-02-0028 Missense FBXW7 1 broad.mit.edu, genome.wustl.edu Yes - FBXW7|chr4:153463593-153463593 Missense gagttGtgtgg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+4 153471357 153471357 TCGA-02-0010 Nonsense FBXW7 1 BCM, broad.mit.edu, genome.wustl.edu Yes - FBXW7|chr4:153471357-153471357 Nonsense ggaggCgagga C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+4 154436236 154436236 TCGA-02-0058 Missense TRIM2 1 BCM No + TRIM2|chr4:154436236-154436236 Missense ggcagCccatg C (other) T Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+4 158462195 158462197 TCGA-06-0213 Inframe_Del GRIA2 1 BCM No + GRIA2|chr4:158462195-158462197 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 1332521 1332521 TCGA-02-0010 Missense TERT 1 genome.wustl.edu No - TERT|chr5:1332521-1332521 Missense gcggcGccccg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 1346683 1346683 TCGA-02-0043 Missense TERT 1 genome.wustl.edu No - TERT|chr5:1346683-1346683 Missense ccgagGaggag G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 67624894 67624894 TCGA-02-0003 Missense PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67624894-67624894 Missense aagggGgaaat G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 67625310 67625312 TCGA-02-0021 Inframe_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67625310-67625312 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 67625370 67625372 TCGA-02-0028 Inframe_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67625370-67625372 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Hypermutated
+5 67626840 67626857 TCGA-06-0178 Inframe_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67626840-67626857 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+5 67626841 67626841 TCGA-02-0089 Missense PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67626841-67626841 Missense aaattGacaaa G (GpA) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 67626855 67626855 TCGA-02-0074 Missense PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67626855-67626855 Missense atgaaCagcat C (other) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 67626884 67626885 TCGA-06-0129 Frameshift_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67626884-67626885 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 67626890 67626892 TCGA-02-0114 Inframe_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67626890-67626892 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Hypermutated
+5 67627006 67627008 TCGA-06-0133 Inframe_Del PIK3R1 1 genome.wustl.edu No + PIK3R1|chr5:67627006-67627008 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+5 96112135 96112135 TCGA-02-0043 Missense CAST 1 broad.mit.edu No + CAST|chr5:96112135-96112135 Missense gccggCtacct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 149477555 149477555 TCGA-02-0114 Missense PDGFRB 1 BCM No - PDGFRB|chr5:149477555-149477555 Missense ccatcCttcgg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 149495455 149495455 TCGA-02-0083 Missense PDGFRB 1 BCM No - PDGFRB|chr5:149495455-149495455 Missense aaatgGccaag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 151029489 151029489 TCGA-02-0010 Missense SPARC 1 broad.mit.edu No - SPARC|chr5:151029489-151029489 Missense ctttgCcacaa C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 179624427 179624427 TCGA-02-0028 Missense MAPK9 1 broad.mit.edu No - MAPK9|chr5:179624427-179624427 Missense taaatGtgttt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 179640065 179640065 TCGA-02-0014 Missense MAPK9 1 broad.mit.edu No - MAPK9|chr5:179640065-179640065 Missense gctctGgggcc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+5 179978410 179978410 TCGA-06-0201 Missense FLT4 1 genome.wustl.edu No - FLT4|chr5:179978410-179978410 Missense accgaGggcgg G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 36212465 36212465 TCGA-02-0083 Missense MAPK13 1 BCM No + MAPK13|chr6:36212465-36212465 Missense acgtgGtgacc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 37247171 37247171 TCGA-02-0011 Missense PIM1 1 BCM No + PIM1|chr6:37247171-37247171 Missense cctcaAtcgcg A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 43083723 43083723 TCGA-02-0069 Missense PPP2R5D 1 broad.mit.edu No + PPP2R5D|chr6:43083723-43083723 Missense tctatGgcaag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 56466808 56466808 TCGA-02-0114 Missense DST 1 genome.wustl.edu No - DST|chr6:56466808-56466808 Missense tgaaaGaaaaa G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 56534115 56534115 TCGA-02-0043 Missense DST 1 genome.wustl.edu No - DST|chr6:56534115-56534115 Missense agacaCctgca C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 56564994 56564994 TCGA-06-0125 Missense DST 1 genome.wustl.edu No - DST|chr6:56564994-56564994 Missense cttatCtgaac C (TpC) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 56576971 56576971 TCGA-06-0145 Missense DST 1 genome.wustl.edu No - DST|chr6:56576971-56576971 Missense atatgGagtat G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 56580657 56580657 TCGA-02-0083 Missense DST 1 genome.wustl.edu No - DST|chr6:56580657-56580657 Missense tgatgGaaaca G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 56581605 56581605 TCGA-02-0010 Missense DST 1 genome.wustl.edu No - DST|chr6:56581605-56581605 Missense ctctgAgaagg A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 56591932 56591932 TCGA-02-0014 Missense DST 1 genome.wustl.edu No - DST|chr6:56591932-56591932 Missense agatgGtttta G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 56607311 56607311 TCGA-06-0148 Missense DST 1 genome.wustl.edu No - DST|chr6:56607311-56607311 Missense tggaaGgtcat G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 69760544 69760544 TCGA-02-0010 Missense BAI3 1 genome.wustl.edu No + BAI3|chr6:69760544-69760544 Missense aagggCaagtt C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 70149531 70149531 TCGA-02-0083 Missense BAI3 1 genome.wustl.edu No + BAI3|chr6:70149531-70149531 Missense atataCcaaat C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 94177152 94177152 TCGA-02-0083 Missense EPHA7 1 BCM No - EPHA7|chr6:94177152-94177152 Missense ctggtCcatta C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 94177566 94177566 TCGA-02-0003 Missense EPHA7 1 BCM No - EPHA7|chr6:94177566-94177566 Missense gatacGaacat G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 108989360 108989360 TCGA-02-0083 Missense FOXO3 1 broad.mit.edu No + FOXO3|chr6:108989360-108989360 Missense ggagcGgcacg G (CpG) C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 117769074 117769074 TCGA-02-0089 Missense ROS1 1 broad.mit.edu No - ROS1|chr6:117769074-117769074 Missense ccttgGttcca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 117790458 117790458 TCGA-02-0114 Splice_site ROS1 1 broad.mit.edu No - ROS1|chr6:117790458-117790458 Other tccagGtatga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+6 142441713 142441713 TCGA-06-0178 Missense NMBR 1 BCM No - NMBR|chr6:142441713-142441713 Missense taaccCcatgg C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+6 142451232 142451232 TCGA-02-0010 Missense NMBR 1 BCM No - NMBR|chr6:142451232-142451232 Missense cctggCggccg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 6005414 6005414 TCGA-02-0028 Nonsense PMS2 1 BCM No - PMS2|chr7:6005414-6005414 Nonsense tggtcCaggtc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 15692146 15692146 TCGA-02-0028 Missense MEOX2 1 genome.wustl.edu No - MEOX2|chr7:15692146-15692146 Missense gggctCcagca C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 17881916 17881916 TCGA-02-0083 Missense SNX13 1 BCM No - SNX13|chr7:17881916-17881916 Missense ggcaaCcttat C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 42046363 42046363 TCGA-02-0083 Missense GLI3 1 BCM No - GLI3|chr7:42046363-42046363 Missense aacagGcacca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 55177569 55177569 TCGA-06-0237 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55177569-55177569 Missense ggtccTtggga T G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55187768 55187768 TCGA-06-0154 Missense EGFR 1 BCM, broad.mit.edu Yes + EGFR|chr7:55187768-55187768 Missense ccgggCgctgc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189204 55189204 TCGA-02-0021 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55189204-55189204 Missense tctgcCgcaaa C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189237 55189237 TCGA-02-0007 Missense EGFR 1 BCM, broad.mit.edu Yes + EGFR|chr7:55189237-55189237 Missense aggacAcctgc A C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189315 55189315 TCGA-02-0089 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55189315-55189315 Missense ttggtGccacc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189316 55189316 TCGA-02-0054 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55189316-55189316 Missense tggtgCcacct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189316 55189316 TCGA-06-0156 Missense EGFR 1 broad.mit.edu Yes + EGFR|chr7:55189316-55189316 Missense tggtgCcacct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189316 55189316 TCGA-06-0148 Missense EGFR 1 broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55189316-55189316 Missense tggtgCcacct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55189316 55189316 TCGA-06-0157 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55189316-55189316 Missense tggtgCcacct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55200533 55200533 TCGA-02-0116 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55200533-55200533 Missense gcccgGcagga G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55200537 55200537 TCGA-06-0125 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55200537-55200537 Missense ggcagGagtca G (GpA) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55200537 55200537 TCGA-02-0046 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu, hgsc.bcm.edu Yes + EGFR|chr7:55200537-55200537 Missense ggcagGagtca G (GpA) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55200603 55200603 TCGA-02-0003 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu, hgsc.bcm.edu Yes + EGFR|chr7:55200603-55200603 Missense cctgtGccatc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55205721 55205721 TCGA-06-0156 Missense EGFR 1 BCM Yes + EGFR|chr7:55205721-55205721 Missense ctcctCctgcc C (TpC) T Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+7 55208201 55208201 TCGA-06-0185 Missense EGFR 1 BCM, genome.wustl.edu Yes + EGFR|chr7:55208201-55208201 Missense ggatgGtgggg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 55208288 55208288 TCGA-02-0010 Missense EGFR 1 BCM, broad.mit.edu, genome.wustl.edu Yes + EGFR|chr7:55208288-55208288 Missense cgctgCggagg C (CpG) G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 79671071 79671071 TCGA-06-0209 Missense GNAI1 1 broad.mit.edu No + GNAI1|chr7:79671071-79671071 Missense tcaaaGatctt G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 93892889 93892889 TCGA-06-0126 Missense COL1A2 1 genome.wustl.edu No + COL1A2|chr7:93892889-93892889 Missense aggtcGcgatg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 95676178 95676178 TCGA-02-0083 Missense SLC25A13 1 broad.mit.edu No - SLC25A13|chr7:95676178-95676178 Missense atattCcattt C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 98391837 98391837 TCGA-02-0114 Missense TRRAP 1 genome.wustl.edu No + TRRAP|chr7:98391837-98391837 Missense agtggGagctg G (GpA) A Valid Valid Valid Validated OK Use_nonsilent Hypermutated
+7 98400280 98400280 TCGA-02-0099 Missense TRRAP 1 genome.wustl.edu No + TRRAP|chr7:98400280-98400280 Missense agatgGtccgg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 98447697 98447697 TCGA-02-0010 Missense TRRAP 1 genome.wustl.edu No + TRRAP|chr7:98447697-98447697 Missense agaggAcacgt A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 99219625 99219625 TCGA-02-0099 Missense CYP3A4 1 genome.wustl.edu No - CYP3A4|chr7:99219625-99219625 Missense tcccaGacttg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 104994978 104994978 TCGA-02-0083 Missense RINT1 1 BCM No + RINT1|chr7:104994978-104994978 Missense ttggcCtaata C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 116168234 116168234 TCGA-02-0114 Nonsense MET 1 BCM, genome.wustl.edu Yes + MET|chr7:116168234-116168234 Nonsense ggctgGtgcca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 116199281 116199281 TCGA-02-0010 Splice_site MET 1 BCM Yes + MET|chr7:116199281-116199281 Other gaaggTatatt T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 116546849 116546849 TCGA-02-0021 Splice_site ST7 1 broad.mit.edu No + ST7|chr7:116546849-116546849 Other gttctAgatat A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 116705516 116705516 TCGA-02-0099 Missense WNT2 1 BCM No - WNT2|chr7:116705516-116705516 Missense gtcagGactgc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 137886376 137886376 TCGA-06-0171 Missense TRIM24 1 BCM No + TRIM24|chr7:137886376-137886376 Missense ccttcGtgcaa G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+7 150327287 150327287 TCGA-02-0114 Missense NOS3 1 genome.wustl.edu No + NOS3|chr7:150327287-150327287 Missense ttgggGgcctg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 150329333 150329333 TCGA-02-0114 Missense NOS3 1 genome.wustl.edu No + NOS3|chr7:150329333-150329333 Missense ccaggGggggc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+7 155288984 155288984 TCGA-06-0124 Missense SHH 1 BCM No - SHH|chr7:155288984-155288984 Missense tctacGtgatc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+8 38391465 38391465 TCGA-02-0060 Missense FGFR1 1 BCM, broad.mit.edu, genome.wustl.edu Yes - FGFR1|chr8:38391465-38391465 Missense ataaaAagaca A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+8 48873436 48873436 TCGA-02-0099 Missense PRKDC 1 genome.wustl.edu No - PRKDC|chr8:48873436-48873436 Missense aaattCcaatg C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 48912493 48912493 TCGA-02-0114 Missense PRKDC 1 genome.wustl.edu No - PRKDC|chr8:48912493-48912493 Missense ggttaCcttca C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 57025643 57025643 TCGA-02-0083 Missense LYN 1 genome.wustl.edu No + LYN|chr8:57025643-57025643 Missense tgtggCcaaac C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 57241776 57241776 TCGA-02-0055 Missense PLAG1 1 BCM, broad.mit.edu, genome.wustl.edu Yes - PLAG1|chr8:57241776-57241776 Missense ctgatGgagtt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+8 75920181 75920181 TCGA-02-0080 Missense PI15 1 broad.mit.edu No + PI15|chr8:75920181-75920181 Missense tttggGccact G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+8 75923999 75923999 TCGA-02-0010 Missense PI15 1 broad.mit.edu No + PI15|chr8:75923999-75923999 Missense atctgTgtttt T A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 91017009 91017009 TCGA-02-0099 Missense NBN 1 genome.wustl.edu No - NBN|chr8:91017009-91017009 Missense acaatCcttat C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 93157428 93157428 TCGA-02-0083 Missense RUNX1T1 1 broad.mit.edu No - RUNX1T1|chr8:93157428-93157428 Missense ttggaGagcac G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+8 120014420 120014420 TCGA-02-0010 Missense TNFRSF11B 1 BCM No - TNFRSF11B|chr8:120014420-120014420 Missense aagggCgctac C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 21827925 21827925 TCGA-06-0156 Missense MTAP 1 broad.mit.edu No + MTAP|chr9:21827925-21827925 Missense cctcaGtcctt G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+9 21961053 21961053 TCGA-02-0010 Missense CDKN2A 1 BCM, genome.wustl.edu Yes - CDKN2A|chr9:21961053-21961053 Missense cggggCgcggc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 21961124 21961125 TCGA-02-0083 Frameshift_Del CDKN2A 1 genome.wustl.edu Yes - CDKN2A|chr9:21961124-21961125 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Hypermutated
+9 21961127 21961128 TCGA-02-0083 Frameshift_Del CDKN2A 1 BCM Yes - CDKN2A|chr9:21961127-21961128 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 21964782 21964782 TCGA-02-0114 Nonsense CDKN2A 1 BCM, genome.wustl.edu Yes - CDKN2A|chr9:21964782-21964782 Nonsense gactgGctggc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 23691590 23691590 TCGA-02-0083 Missense ELAVL2 1 genome.wustl.edu No - ELAVL2|chr9:23691590-23691590 Missense aagggGtgtag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 34542713 34542713 TCGA-02-0083 Missense CNTFR 1 BCM No - CNTFR|chr9:34542713-34542713 Missense ctggaCtgagg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 36836902 36836902 TCGA-06-0214 Missense PAX5 1 genome.wustl.edu No - PAX5|chr9:36836902-36836902 Missense tccctAcagcc A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+9 74974800 74974800 TCGA-02-0028 Missense ANXA1 1 BCM No + ANXA1|chr9:74974800-74974800 Missense caaagGagatt G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 93527042 93527042 TCGA-02-0083 Missense ROR2 1 BCM No - ROR2|chr9:93527042-93527042 Missense tgcggGaggag G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 93535351 93535351 TCGA-02-0010 Missense ROR2 1 BCM No - ROR2|chr9:93535351-93535351 Missense ccatcGcccgc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 97249179 97249179 TCGA-06-0125 Nonsense PTCH1 1 BCM No - PTCH1|chr9:97249179-97249179 Nonsense accccCgaggg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+9 109287936 109287936 TCGA-02-0010 Missense KLF4 1 genome.wustl.edu No - KLF4|chr9:109287936-109287936 Missense cggggCaccgc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 109289919 109289919 TCGA-02-0010 Missense KLF4 1 genome.wustl.edu No - KLF4|chr9:109289919-109289919 Missense acgacGtgagc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 116837402 116837402 TCGA-06-0188 Missense TNC 1 broad.mit.edu No - TNC|chr9:116837402-116837402 Missense ctactGaggtt G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+9 116878675 116878675 TCGA-02-0083 Missense TNC 1 broad.mit.edu No - TNC|chr9:116878675-116878675 Missense aacagGcctcg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 116888335 116888335 TCGA-02-0010 Missense TNC 1 broad.mit.edu No - TNC|chr9:116888335-116888335 Missense ggatcGccaat G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 134761810 134761810 TCGA-02-0114 Missense TSC1 1 genome.wustl.edu No - TSC1|chr9:134761810-134761810 Missense cagcaGcgagc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 135631024 135631024 TCGA-02-0114 Splice_site VAV2 1 genome.wustl.edu No - VAV2|chr9:135631024-135631024 Other caccaGccgcc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 138509420 138509420 TCGA-02-0114 Missense NOTCH1 1 genome.wustl.edu No - NOTCH1|chr9:138509420-138509420 Missense gctgaCcccgg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+9 138510658 138510658 TCGA-02-0083 Missense NOTCH1 1 genome.wustl.edu No - NOTCH1|chr9:138510658-138510658 Missense gcctgGcggtg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 3814279 3814279 TCGA-02-0114 Missense KLF6 1 genome.wustl.edu No - KLF6|chr10:3814279-3814279 Missense ggaatCcgaac C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 3817172 3817172 TCGA-02-0010 Missense KLF6 1 genome.wustl.edu No - KLF6|chr10:3817172-3817172 Missense ccaggAgctcc A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 8140468 8140468 TCGA-02-0010 Missense GATA3 1 genome.wustl.edu No + GATA3|chr10:8140468-8140468 Missense gccacGccagc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 8155865 8155865 TCGA-02-0028 Missense GATA3 1 genome.wustl.edu No + GATA3|chr10:8155865-8155865 Missense gtcctCcctga C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 12038348 12038348 TCGA-02-0083 Missense UPF2 1 broad.mit.edu No - UPF2|chr10:12038348-12038348 Missense tgttaGaagat G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 12199705 12199705 TCGA-02-0114 Missense DHTKD1 1 broad.mit.edu No + DHTKD1|chr10:12199705-12199705 Missense aaatgGcacca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 12331616 12331616 TCGA-06-0141 Missense CDC123 1 broad.mit.edu No + CDC123|chr10:12331616-12331616 Missense acagtGaagtg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 26865111 26865111 TCGA-06-0154 Missense APBB1IP 1 broad.mit.edu No + APBB1IP|chr10:26865111-26865111 Missense ttttaCgggct C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 29011215 29011215 TCGA-02-0114 Missense BAMBI 1 genome.wustl.edu No + BAMBI|chr10:29011215-29011215 Missense cagtgGgcacg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 31831344 31831344 TCGA-02-0114 Missense ZEB1 1 genome.wustl.edu No + ZEB1|chr10:31831344-31831344 Missense ttgaaGagttt G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 50497778 50497778 TCGA-02-0083 Missense CHAT 1 BCM No + CHAT|chr10:50497778-50497778 Missense ccaggGgctgc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 50505694 50505694 TCGA-06-0125 Missense CHAT 1 BCM No + CHAT|chr10:50505694-50505694 Missense ccgccGtctca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 74826987 74826987 TCGA-02-0083 Missense ANXA7 1 broad.mit.edu No - ANXA7|chr10:74826987-74826987 Missense ttctgGgtatc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 76407199 76407199 TCGA-02-0114 Missense MYST4 1 broad.mit.edu No + MYST4|chr10:76407199-76407199 Missense cttggGaggta G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 76459177 76459177 TCGA-02-0043 Missense MYST4 1 broad.mit.edu No + MYST4|chr10:76459177-76459177 Missense agaggGaaacc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 89643789 89643789 TCGA-06-0184 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89643789-89643789 Missense tatggGatttc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89680799 89680800 TCGA-06-0197 Frameshift_Del PTEN 1 BCM Yes + PTEN|chr10:89680799-89680800 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89680800 89680801 TCGA-06-0157 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89680800-89680801 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+10 89680800 89680801 TCGA-06-0197 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89680800-89680801 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+10 89680805 89680806 TCGA-02-0052 Frameshift_Del PTEN 1 BCM, genome.wustl.edu Yes + PTEN|chr10:89680805-89680806 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682772 89682772 TCGA-06-0190 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682772-89682772 Missense gaagaCcataa C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682783 89682783 TCGA-02-0014 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682783-89682783 Missense cccacCacagc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 89682810 89682811 TCGA-06-0156 Frameshift_Del PTEN 1 BCM Yes + PTEN|chr10:89682810-89682811 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682884 89682884 TCGA-06-0138 Nonsense PTEN 1 BCM, broad.mit.edu Yes + PTEN|chr10:89682884-89682884 Nonsense agggaCgaact C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682884 89682884 TCGA-06-0176 Nonsense PTEN 1 BCM, broad.mit.edu Yes + PTEN|chr10:89682884-89682884 Nonsense agggaCgaact C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682885 89682885 TCGA-02-0027 Frameshift_Del PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682885-89682885 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682887 89682887 TCGA-02-0055 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682887-89682887 Missense gacgaActggt A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682891 89682891 TCGA-06-0187 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682891-89682891 Missense aactgGtgtaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89682971 89682971 TCGA-02-0001 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89682971-89682971 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+10 89682972 89682972 TCGA-06-0195 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89682972-89682972 Missense agtaaGgacca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89701862 89701862 TCGA-06-0166 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89701862-89701862 Missense agtaaCtattc C (other) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89701862 89701862 TCGA-02-0021 Missense PTEN 1 BCM Yes + PTEN|chr10:89701862-89701862 Missense agtaaCtattc C (other) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89701879 89701879 TCGA-02-0038 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89701879-89701879 Missense agaggCgctat C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89701893 89701893 TCGA-02-0099 Nonsense PTEN 1 broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89701893-89701893 Nonsense tattaTtatag T G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 89701940 89701940 TCGA-02-0007 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89701940-89701940 Missense ggcacTgttgt T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89707658 89707658 TCGA-02-0113 Nonsense PTEN 1 BCM, genome.wustl.edu Yes + PTEN|chr10:89707658-89707658 Nonsense gacggGaagac G (GpA) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89707676 89707676 TCGA-02-0075 Missense PTEN 1 BCM, broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89707676-89707676 Missense tgtacTttgag T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710659 89710659 TCGA-06-0124 Missense PTEN 1 BCM, genome.wustl.edu Yes + PTEN|chr10:89710659-89710659 Missense aaataCattct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710781 89710784 TCGA-06-0125 Frameshift_Del PTEN 1 BCM Yes + PTEN|chr10:89710781-89710784 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710784 89710787 TCGA-06-0125 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89710784-89710787 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710784 89710787 TCGA-06-0206 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89710784-89710787 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710788 89710788 TCGA-02-0071 Nonsense PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89710788-89710788 Nonsense tacttTaacaa T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 89710797 89710797 TCGA-06-0188 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89710797-89710797 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+10 89710811 89710815 TCGA-06-0168 Frameshift_Del PTEN 1 genome.wustl.edu Yes + PTEN|chr10:89710811-89710815 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+10 89710832 89710832 TCGA-06-0213 Nonsense PTEN 1 broad.mit.edu, genome.wustl.edu Yes + PTEN|chr10:89710832-89710832 Nonsense ccaacCgatac C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 123288210 123288210 TCGA-02-0033 Missense FGFR2 1 genome.wustl.edu No - FGFR2|chr10:123288210-123288210 Missense gaaacCagcac C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+10 124348403 124348403 TCGA-02-0028 Missense DMBT1 1 genome.wustl.edu No + DMBT1|chr10:124348403-124348403 Missense tgatgCcaatg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 128009005 128009005 TCGA-02-0010 Missense ADAM12 1 genome.wustl.edu No - ADAM12|chr10:128009005-128009005 Missense tggggAcctct A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+10 129073048 129073048 TCGA-02-0010 Missense DOCK1 1 broad.mit.edu No + DOCK1|chr10:129073048-129073048 Missense gtggtCggagg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 6426862 6426862 TCGA-06-0122 Missense TRIM3 1 broad.mit.edu No - TRIM3|chr11:6426862-6426862 Missense ccactGcttta G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+11 6434421 6434421 TCGA-02-0083 Missense TRIM3 1 broad.mit.edu No - TRIM3|chr11:6434421-6434421 Missense cggacGgcacg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 6586561 6586561 TCGA-02-0010 Missense ILK 1 BCM No + ILK|chr11:6586561-6586561 Missense tgtggAcaaag A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 9552534 9552534 TCGA-06-0190 Missense WEE1 1 BCM No + WEE1|chr11:9552534-9552534 Missense gggcgGgcgaa G (other) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+11 18380975 18380975 TCGA-02-0083 Missense LDHA 1 genome.wustl.edu No + LDHA|chr11:18380975-18380975 Missense cttgaCctacg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 18381850 18381850 TCGA-02-0014 Missense LDHA 1 genome.wustl.edu No + LDHA|chr11:18381850-18381850 Missense tggtgTctctc T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 107611687 107611687 TCGA-02-0010 Missense ATM 1 broad.mit.edu No + ATM|chr11:107611687-107611687 Missense tttacGgagct G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 107620796 107620796 TCGA-02-0010 Missense ATM 1 broad.mit.edu No + ATM|chr11:107620796-107620796 Missense ggctgTcaact T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 111095932 111095932 TCGA-02-0114 Missense SNF1LK2 1 broad.mit.edu No + SNF1LK2|chr11:111095932-111095932 Missense gcctgGggcag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 111096956 111096956 TCGA-06-0176 Missense SNF1LK2 1 broad.mit.edu No + SNF1LK2|chr11:111096956-111096956 Missense gccggCggctc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+11 118654485 118654485 TCGA-02-0083 Missense CBL 1 broad.mit.edu No + CBL|chr11:118654485-118654485 Missense tgaacCcatcg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 118661372 118661372 TCGA-02-0083 Nonsense CBL 1 broad.mit.edu No + CBL|chr11:118661372-118661372 Nonsense ccctgGacagg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 125008322 125008322 TCGA-06-0145 Missense CHEK1 1 BCM No + CHEK1|chr11:125008322-125008322 Missense taatcGtgagc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+11 125028953 125028953 TCGA-02-0043 Splice_site CHEK1 1 BCM No + CHEK1|chr11:125028953-125028953 Other ctaagGtattt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 128143273 128143273 TCGA-02-0114 Missense FLI1 1 broad.mit.edu No + FLI1|chr11:128143273-128143273 Missense gggcgGaggcg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+11 128186040 128186040 TCGA-02-0009 Missense FLI1 1 broad.mit.edu No + FLI1|chr11:128186040-128186040 Missense ccaacGtcccc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 6630758 6630758 TCGA-02-0083 Missense ING4 1 broad.mit.edu No - ING4|chr12:6630758-6630758 Missense ctcggGggaaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 6630798 6630798 TCGA-02-0114 Nonsense ING4 1 broad.mit.edu No - ING4|chr12:6630798-6630798 Nonsense gagtgGttcca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 6647395 6647395 TCGA-02-0114 Missense ZNF384 1 genome.wustl.edu No - ZNF384|chr12:6647395-6647395 Missense cccagGcccag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 6652748 6652748 TCGA-02-0114 Missense ZNF384 1 genome.wustl.edu No - ZNF384|chr12:6652748-6652748 Missense cagctCctacc C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 9116623 9116623 TCGA-02-0028 Missense A2M 1 genome.wustl.edu No - A2M|chr12:9116623-9116623 Missense gcaaaTtccaa T C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 9150104 9150104 TCGA-02-0024 Missense A2M 1 genome.wustl.edu No - A2M|chr12:9150104-9150104 Missense tctttGggcag G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 25289551 25289551 TCGA-02-0069 Missense KRAS 1 genome.wustl.edu No - KRAS|chr12:25289551-25289551 Missense agctgGtggcg G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 43212631 43212631 TCGA-02-0083 Missense NELL2 1 broad.mit.edu No - NELL2|chr12:43212631-43212631 Missense gtgaaGgtcag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 54780232 54780232 TCGA-02-0083 Missense ERBB3 1 BCM No + ERBB3|chr12:54780232-54780232 Missense ccagaGccttt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 56151942 56151942 TCGA-06-0133 Missense GLI1 1 broad.mit.edu No + GLI1|chr12:56151942-56151942 Missense tgtggCtattc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 56288721 56288721 TCGA-02-0107 Missense DTX3 1 broad.mit.edu No + DTX3|chr12:56288721-56288721 Missense cacagGgagac G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 56407992 56407992 TCGA-02-0014 Missense CENTG1 1 BCM No - CENTG1|chr12:56407992-56407992 Missense gcaagGtcaag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 56408033 56408033 TCGA-02-0043 Missense CENTG1 1 BCM No - CENTG1|chr12:56408033-56408033 Missense cgagaGtcaga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 56444898 56444898 TCGA-02-0043 Missense CYP27B1 1 BCM, broad.mit.edu, genome.wustl.edu Yes - CYP27B1|chr12:56444898-56444898 Missense gtctgGggcgc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 56445112 56445112 TCGA-02-0080 Missense CYP27B1 1 BCM, genome.wustl.edu Yes - CYP27B1|chr12:56445112-56445112 Missense ttgtgCctggg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 56482213 56482213 TCGA-02-0114 Nonsense AVIL 1 broad.mit.edu No - AVIL|chr12:56482213-56482213 Nonsense atttgGagtgt G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 63175611 63175611 TCGA-02-0114 Missense TBK1 1 broad.mit.edu No + TBK1|chr12:63175611-63175611 Missense cagacGcatgg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 67516737 67516737 TCGA-02-0085 Missense MDM2 1 broad.mit.edu No + MDM2|chr12:67516737-67516737 Missense ctgtgTatcag T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 108019967 108019967 TCGA-02-0083 Missense UNG 1 BCM No + UNG|chr12:108019967-108019967 Missense gcgtgGctggg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 111372572 111372572 TCGA-02-0028 Missense PTPN11 1 genome.wustl.edu No + PTPN11|chr12:111372572-111372572 Missense gagggGagaaa G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 111395220 111395220 TCGA-06-0171 Missense PTPN11 1 genome.wustl.edu No + PTPN11|chr12:111395220-111395220 Missense aacatCctgcc C (TpC) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 117103657 117103657 TCGA-02-0075 Missense TAOK3 1 broad.mit.edu No - TAOK3|chr12:117103657-117103657 Missense agcacCgcctc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+12 119280036 119280036 TCGA-02-0083 Missense MSI1 1 broad.mit.edu No - MSI1|chr12:119280036-119280036 Missense agtgtGtgaaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 119286911 119286911 TCGA-02-0114 Missense MSI1 1 broad.mit.edu No - MSI1|chr12:119286911-119286911 Missense ggcgaGcacag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 121222973 121222973 TCGA-02-0083 Nonsense IL31 1 genome.wustl.edu No - IL31|chr12:121222973-121222973 Nonsense gttttCagagt C (TpC) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 131012246 131012246 TCGA-02-0083 Nonsense EP400 1 BCM No + EP400|chr12:131012246-131012246 Nonsense agatgCaggct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 131076211 131076211 TCGA-02-0114 Missense EP400 1 BCM No + EP400|chr12:131076211-131076211 Missense gtgatGcagac G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+12 131094732 131094732 TCGA-02-0114 Missense EP400 1 BCM No + EP400|chr12:131094732-131094732 Missense tgcagGagagg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+13 27829760 27829760 TCGA-06-0173 Missense FLT1 1 BCM No - FLT1|chr13:27829760-27829760 Missense atgaaGgtgtc G (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 31788650 31788650 TCGA-02-0010 Missense BRCA2 1 broad.mit.edu No + BRCA2|chr13:31788650-31788650 Missense gacacGctgca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+13 31809250 31809250 TCGA-06-0169 Missense BRCA2 1 broad.mit.edu No + BRCA2|chr13:31809250-31809250 Missense acgaaCccatt C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 31809542 31809542 TCGA-02-0014 Missense BRCA2 1 broad.mit.edu No + BRCA2|chr13:31809542-31809542 Missense ggaaaTcaagc T G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+13 47834984 47834984 TCGA-06-0176 Nonsense RB1 1 BCM, broad.mit.edu Yes + RB1|chr13:47834984-47834984 Nonsense cacctCgaaca C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47835032 47835069 TCGA-02-0055 Frameshift_Del RB1 1 BCM, genome.wustl.edu Yes + RB1|chr13:47835032-47835069 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+13 47845597 47845597 TCGA-06-0195 Nonsense RB1 1 BCM, broad.mit.edu Yes + RB1|chr13:47845597-47845597 Nonsense gtgatCaacct C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47925250 47925250 TCGA-02-0052 Splice_site RB1 1 BCM, broad.mit.edu, genome.wustl.edu Yes + RB1|chr13:47925250-47925250 Other atatgTaagca T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47928486 47928486 TCGA-06-0213 Missense RB1 1 BCM Yes + RB1|chr13:47928486-47928486 Missense aaaaaGgttag G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47931824 47931824 TCGA-06-0184 Splice_site RB1 1 BCM, broad.mit.edu Yes + RB1|chr13:47931824-47931824 Other ccacaGtgtat G (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47931840 47931840 TCGA-06-0184 Missense RB1 1 BCM, broad.mit.edu Yes + RB1|chr13:47931840-47931840 Missense agcctAtctcc A T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47931968 47931968 TCGA-02-0033 Nonsense RB1 1 BCM, genome.wustl.edu Yes + RB1|chr13:47931968-47931968 Nonsense tggacCaagta C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47937375 47937375 TCGA-02-0007 Nonsense RB1 1 BCM, broad.mit.edu, genome.wustl.edu Yes + RB1|chr13:47937375-47937375 Nonsense ttcctCgaagc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 47945496 47945496 TCGA-06-0206 Splice_site RB1 1 BCM, broad.mit.edu Yes + RB1|chr13:47945496-47945496 Other tgacaGaatct G (GpA) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 94484895 94484895 TCGA-02-0083 Missense ABCC4 1 broad.mit.edu No - ABCC4|chr13:94484895-94484895 Missense gcaagGcagaa G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+13 94613377 94613377 TCGA-02-0037 Missense ABCC4 1 broad.mit.edu No - ABCC4|chr13:94613377-94613377 Missense attcaGgtaaa G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+13 113008879 113008879 TCGA-02-0083 Missense LAMP1 1 broad.mit.edu No + LAMP1|chr13:113008879-113008879 Missense cttctCtgctg C (TpC) G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+13 113021973 113021973 TCGA-02-0116 Splice_site LAMP1 1 broad.mit.edu No + LAMP1|chr13:113021973-113021973 Other acacgGtaggg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+14 55148856 55148856 TCGA-02-0083 Missense KTN1 1 broad.mit.edu No + KTN1|chr14:55148856-55148856 Missense ttaggGaaaga G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+14 59263887 59263887 TCGA-02-0021 Missense RTN1 1 broad.mit.edu No - RTN1|chr14:59263887-59263887 Missense ggccgCggagg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+14 94150664 94150664 TCGA-06-0209 Missense SERPINA3 1 genome.wustl.edu No + SERPINA3|chr14:94150664-94150664 Missense cacacGtggac G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+14 101617806 101617806 TCGA-02-0010 Missense HSP90AA1 1 BCM No - HSP90AA1|chr14:101617806-101617806 Missense agtagActaat A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+14 101675353 101675353 TCGA-02-0083 Missense HSP90AA1 1 BCM No - HSP90AA1|chr14:101675353-101675353 Missense cgccgCcgttt C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 32316305 32316305 TCGA-06-0133 Missense SLC12A6 1 BCM No - SLC12A6|chr15:32316305-32316305 Missense agcatGacagt G (GpA) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+15 32317006 32317006 TCGA-02-0102 Missense SLC12A6 1 BCM No - SLC12A6|chr15:32317006-32317006 Missense agtagCccaat C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+15 55330914 55330914 TCGA-02-0114 Splice_site TCF12 1 BCM No + TCF12|chr15:55330914-55330914 Other ccctgGtaaga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 55341606 55341607 TCGA-02-0114 Frameshift_Del TCF12 1 BCM No + TCF12|chr15:55341606-55341607 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 55342601 55342601 TCGA-06-0128 Splice_site TCF12 1 BCM No + TCF12|chr15:55342601-55342601 Other tgttaGgtggc G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+15 72077554 72077554 TCGA-02-0083 Missense PML 1 genome.wustl.edu No + PML|chr15:72077554-72077554 Missense cctggCcccta C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 77008808 77008808 TCGA-02-0043 Splice_site CTSH 1 genome.wustl.edu No - CTSH|chr15:77008808-77008808 Other gcaagGtaact G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 82233332 82233332 TCGA-02-0028 Nonsense ADAMTSL3 1 BCM No + ADAMTSL3|chr15:82233332-82233332 Nonsense gcttgGggcga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 82481336 82481336 TCGA-02-0083 Missense ADAMTSL3 1 BCM No + ADAMTSL3|chr15:82481336-82481336 Missense tccggGactgc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 86528499 86528499 TCGA-02-0043 Missense NTRK3 1 genome.wustl.edu No - NTRK3|chr15:86528499-86528499 Missense gctcaAcgccg A G Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 88818012 88818012 TCGA-02-0083 Missense IQGAP1 1 BCM No + IQGAP1|chr15:88818012-88818012 Missense gcgctCccaca C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 88818856 88818856 TCGA-02-0075 Missense IQGAP1 1 BCM No + IQGAP1|chr15:88818856-88818856 Missense taaccAgcagc A G Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+15 89225202 89225202 TCGA-02-0010 Missense FURIN 1 genome.wustl.edu No + FURIN|chr15:89225202-89225202 Missense gcaccGcccct G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 89225687 89225687 TCGA-02-0028 Missense FURIN 1 genome.wustl.edu No + FURIN|chr15:89225687-89225687 Missense aggggCcggcc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+15 89225991 89225991 TCGA-02-0010 Missense FURIN 1 genome.wustl.edu No + FURIN|chr15:89225991-89225991 Missense ccgtgGcctca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 2038750 2038750 TCGA-02-0047 Missense TSC2 1 genome.wustl.edu No + TSC2|chr16:2038750-2038750 Missense aaataCtgaga C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+16 2064367 2064367 TCGA-02-0010 Missense TSC2 1 genome.wustl.edu No + TSC2|chr16:2064367-2064367 Missense tggccGtccca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 2070190 2070190 TCGA-02-0010 Missense TSC2 1 genome.wustl.edu No + TSC2|chr16:2070190-2070190 Missense ttggcGccctg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 2290056 2290056 TCGA-02-0043 Missense ABCA3 1 genome.wustl.edu No - ABCA3|chr16:2290056-2290056 Missense tgaagCcgagc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 11256592 11256592 TCGA-02-0114 Missense SOCS1 1 genome.wustl.edu No - SOCS1|chr16:11256592-11256592 Missense ctgggGgcccc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 24138810 24138810 TCGA-06-0185 Missense PRKCB1 1 broad.mit.edu No + PRKCB1|chr16:24138810-24138810 Missense acttcGacaaa G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+16 49341571 49341571 TCGA-02-0114 Missense CYLD 1 genome.wustl.edu No + CYLD|chr16:49341571-49341571 Missense gttagCagaga C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 65554895 65554895 TCGA-06-0139 Missense CES3 1 genome.wustl.edu No + CES3|chr16:65554895-65554895 Missense cacagGtgcct G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+16 65555760 65555760 TCGA-02-0114 Splice_site CES3 1 genome.wustl.edu No + CES3|chr16:65555760-65555760 Other ccccaGcactg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+16 73821184 73821184 TCGA-06-0176 Missense BCAR1 1 BCM No - BCAR1|chr16:73821184-73821184 Missense tgtggCgcaca C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+16 73821401 73821401 TCGA-02-0099 Missense BCAR1 1 BCM No - BCAR1|chr16:73821401-73821401 Missense gactgGaacag G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7514728 7514728 TCGA-02-0024 Nonsense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7514728-7514728 Nonsense tgttcCgagag C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517636 7517636 TCGA-06-0128 Frameshift_Del TP53 1 BCM Yes - TP53|chr17:7517636-7517636 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517651 7517651 TCGA-06-0188 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7517651-7517651 Missense cctagCactgc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517652 7517652 TCGA-06-0188 Splice_site TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7517652-7517652 Other tcctaGcactg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517819 7517819 TCGA-02-0003 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517819-7517819 Missense gagacCggcgc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517819 7517819 TCGA-02-0046 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517819-7517819 Missense gagacCggcgc C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517821 7517821 TCGA-06-0195 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517821-7517821 Missense gagagAccggc A C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517830 7517830 TCGA-02-0001 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7517830-7517830 Missense ctgtcCtggga C (other) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517831 7517831 TCGA-02-0083 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7517831-7517831 Missense cctgtCctggg C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7517836 7517836 TCGA-02-0114 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517836-7517836 Missense ttgtgCctgtc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7517845 7517845 TCGA-06-0206 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7517845-7517845 Missense ggtgcGtgttt G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517846 7517846 TCGA-02-0080 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517846-7517846 Missense aggtgCgtgtt C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517846 7517846 TCGA-02-0010 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517846-7517846 Missense aggtgCgtgtt C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7517849 7517849 TCGA-02-0058 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517849-7517849 Missense ttgagGtgcgt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517854 7517854 TCGA-06-0197 Missense TP53 1 broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517854-7517854 Missense cagctTtgagg T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7517867 7517867 TCGA-06-0195 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7517867-7517867 Missense tactgGgacgg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518234 7518234 TCGA-02-0034 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7518234-7518234 Missense cactgGaagac G (GpA) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518263 7518263 TCGA-02-0033 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7518263-7518263 Missense gaaccGgaggc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518263 7518263 TCGA-06-0241 Missense TP53 1 BCM, genome.wustl.edu Yes - TP53|chr17:7518263-7518263 Missense gaaccGgaggc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518273 7518273 TCGA-06-0190 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7518273-7518273 Missense tgggcGgcatg G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518303 7518303 TCGA-02-0074 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7518303-7518303 Missense actacAactac A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518928 7518928 TCGA-02-0055 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7518928-7518928 Missense atagtGtggtg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518937 7518937 TCGA-02-0054 Nonsense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7518937-7518937 Nonsense cttttCgacat C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7518974 7518975 TCGA-02-0014 Frameshift_Del TP53 1 genome.wustl.edu Yes - TP53|chr17:7518974-7518975 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7518990 7518990 TCGA-06-0237 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7518990-7518990 Missense tcttaTccgag T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519120 7519120 TCGA-02-0089 Missense TP53 1 broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519120-7519120 Missense cccacCatgag C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519121 7519121 TCGA-02-0003 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519121-7519121 Missense ccccaCcatga C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519126 7519126 TCGA-02-0046 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519126-7519126 Missense gctgcCcccac C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519128 7519128 TCGA-02-0114 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519128-7519128 Missense gcgctGccccc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7519131 7519131 TCGA-02-0010 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519131-7519131 Missense gaggcGctgcc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 7519131 7519131 TCGA-02-0037 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519131-7519131 Missense gaggcGctgcc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519132 7519132 TCGA-02-0011 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519132-7519132 Missense tgaggCgctgc C (CpG) G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519182 7519182 TCGA-06-0130 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519182-7519182 Missense cgtccGcgcca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519182 7519182 TCGA-06-0184 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519182-7519182 Missense cgtccGcgcca G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519237 7519238 TCGA-06-0221 Frameshift_Del TP53 1 genome.wustl.edu Yes - TP53|chr17:7519237-7519238 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519251 7519251 TCGA-02-0034 Missense TP53 1 BCM Yes - TP53|chr17:7519251-7519251 Missense gttttGccaac G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7519267 7519267 TCGA-02-0075 Missense TP53 1 BCM, broad.mit.edu, genome.wustl.edu Yes - TP53|chr17:7519267-7519267 Missense ctgccCtcaac C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 7520118 7520122 TCGA-06-0156 Frameshift_Del TP53 1 BCM Yes - TP53|chr17:7520118-7520122 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 8051651 8051651 TCGA-02-0114 Missense AURKB 1 broad.mit.edu No - AURKB|chr17:8051651-8051651 Missense agaagGtgatg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 19225977 19225977 TCGA-02-0014 Missense MAPK7 1 genome.wustl.edu No + MAPK7|chr17:19225977-19225977 Missense cccctGcccca G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 26574560 26574598 TCGA-02-0001 Splice_site NF1 1 genome.wustl.edu No + NF1|chr17:26574560-26574598 Other atgctAgtaac A Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+17 26580304 26580304 TCGA-02-0075 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26580304-26580304 Nonsense ttgggGgagtg G (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26581118 26581118 TCGA-02-0028 Missense NF1 1 genome.wustl.edu No + NF1|chr17:26581118-26581118 Missense ggtcaGgtaag G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 26609550 26609550 TCGA-02-0107 Missense NF1 1 genome.wustl.edu No + NF1|chr17:26609550-26609550 Missense ctcagAtttat A T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26610175 26610175 TCGA-02-0033 Splice_site NF1 1 genome.wustl.edu No + NF1|chr17:26610175-26610175 Other gtgtaGatact G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26610182 26610182 TCGA-06-0190 Missense NF1 1 genome.wustl.edu No + NF1|chr17:26610182-26610182 Missense tacttCagagt C (TpC) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26612877 26612877 TCGA-06-0201 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26612877-26612877 Nonsense gaagaCgacct C (CpG) T Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+17 26677105 26677108 TCGA-02-0107 Frameshift_Del NF1 1 genome.wustl.edu No + NF1|chr17:26677105-26677108 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26677114 26677114 TCGA-02-0115 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26677114-26677114 Nonsense aagtgGtttgt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26678919 26678919 TCGA-06-0214 Missense NF1 1 genome.wustl.edu No + NF1|chr17:26678919-26678919 Missense caaaaGatgtc G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26678984 26678984 TCGA-06-0201 Splice_site NF1 1 genome.wustl.edu No + NF1|chr17:26678984-26678984 Other ttacgGtaggt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26686128 26686128 TCGA-06-0124 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26686128-26686128 Nonsense aaaaaCagatg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26687479 26687479 TCGA-02-0086 Frameshift_Del NF1 1 genome.wustl.edu No + NF1|chr17:26687479-26687479 Other Indel Indel Indel Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+17 26688511 26688511 TCGA-02-0028 Splice_site NF1 1 genome.wustl.edu No + NF1|chr17:26688511-26688511 Other ttacaGaagag G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 26689934 26689934 TCGA-06-0184 Frameshift_Del NF1 1 genome.wustl.edu No + NF1|chr17:26689934-26689934 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26691678 26691678 TCGA-02-0028 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26691678-26691678 Nonsense ttttgGgtagc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 26691722 26691722 TCGA-06-0124 Nonsense NF1 1 genome.wustl.edu No + NF1|chr17:26691722-26691722 Nonsense gtattCagcag C (TpC) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 26691733 26691733 TCGA-02-0010 Missense NF1 1 genome.wustl.edu No + NF1|chr17:26691733-26691733 Missense gtaccGcactt G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 26691739 26691739 TCGA-02-0086 Frameshift_Del NF1 1 genome.wustl.edu No + NF1|chr17:26691739-26691739 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35116841 35116841 TCGA-02-0080 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35116841-35116841 Missense ccaccTctacc T ? Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35116922 35116922 TCGA-02-0115 Splice_site ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35116922-35116922 Other gcaggTgaggc T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35119867 35119867 TCGA-02-0069 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35119867-35119867 Missense cagtgAcgcgc A T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35121736 35121736 TCGA-02-0089 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35121736-35121736 Missense gatccTgcacc T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35121760 35121760 TCGA-02-0116 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35121760-35121760 Missense tgcacAaccaa A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35121767 35121767 TCGA-02-0089 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35121767-35121767 Missense ccaagAggtga A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35121782 35121782 TCGA-02-0115 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35121782-35121782 Missense agaggAtggaa A G Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35121805 35121805 TCGA-02-0115 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35121805-35121805 Missense agaagTgcagc T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35133731 35133731 TCGA-02-0107 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35133731-35133731 Missense tccagTggcca T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35134527 35134527 TCGA-02-0069 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35134527-35134527 Missense tggtgTgggct T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 35134527 35134527 TCGA-02-0113 Missense ERBB2 1 genome.wustl.edu No + ERBB2|chr17:35134527-35134527 Missense tggtgTgggct T C Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+17 37735120 37735121 TCGA-02-0114 Frameshift_Del STAT3 1 BCM No - STAT3|chr17:37735120-37735121 Other Indel Indel Indel Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 42723325 42723325 TCGA-06-0141 Missense ITGB3 1 broad.mit.edu No + ITGB3|chr17:42723325-42723325 Missense aaatcCgttct C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 42724694 42724694 TCGA-02-0083 Missense ITGB3 1 broad.mit.edu No + ITGB3|chr17:42724694-42724694 Missense gtgtgGggtat G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 42742529 42742529 TCGA-02-0010 Missense ITGB3 1 broad.mit.edu No + ITGB3|chr17:42742529-42742529 Missense agaggCcacgt C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 45539183 45539183 TCGA-02-0043 Missense PDK2 1 BCM No + PDK2|chr17:45539183-45539183 Missense ccaacCcagcc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 45619111 45619111 TCGA-02-0043 Missense COL1A1 1 BCM No - COL1A1|chr17:45619111-45619111 Missense ccaccCtcaag C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 45623200 45623200 TCGA-02-0083 Missense COL1A1 1 BCM No - COL1A1|chr17:45623200-45623200 Missense ctggcCctgct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 45628312 45628312 TCGA-02-0083 Missense COL1A1 1 BCM No - COL1A1|chr17:45628312-45628312 Missense gtcctCctggc C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 45630091 45630091 TCGA-02-0043 Splice_site COL1A1 1 BCM No - COL1A1|chr17:45630091-45630091 Other atgatGtaagt G (other) Indel Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 62215542 62215542 TCGA-02-0083 Missense PRKCA 1 broad.mit.edu No + PRKCA|chr17:62215542-62215542 Missense agccaCcattc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 63463748 63463748 TCGA-06-0141 Missense KPNA2 1 broad.mit.edu No + KPNA2|chr17:63463748-63463748 Missense tgcccGtcttc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+17 74363373 74363373 TCGA-02-0083 Nonsense TIMP2 1 BCM No - TIMP2|chr17:74363373-74363373 Nonsense ccaagCaggag C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+17 74479447 74479447 TCGA-02-0028 Missense LGALS3BP 1 broad.mit.edu No - LGALS3BP|chr17:74479447-74479447 Missense acaaaGccctg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+18 41700876 41700876 TCGA-02-0083 Missense KIAA1632 1 BCM No - KIAA1632|chr18:41700876-41700876 Missense tttcaGcagcc G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+18 42074101 42074101 TCGA-02-0099 Missense C18orf25 1 genome.wustl.edu No + C18orf25|chr18:42074101-42074101 Missense cacagGagcta G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+18 46858703 46858703 TCGA-02-0028 Nonsense SMAD4 1 broad.mit.edu No + SMAD4|chr18:46858703-46858703 Nonsense ggctgGggacc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+18 58790915 58790915 TCGA-06-0176 Missense PHLPP 1 broad.mit.edu No + PHLPP|chr18:58790915-58790915 Missense tgtcaTgcaaa T C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+18 59136627 59136627 TCGA-02-0089 Missense BCL2 1 genome.wustl.edu No - BCL2|chr18:59136627-59136627 Missense ggcctGcgctc G (other) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+19 7244845 7244845 TCGA-06-0147 Missense INSR 1 BCM No - INSR|chr19:7244845-7244845 Missense tggccGcgctg G (CpG) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+19 40903582 40903582 TCGA-02-0057 Missense MLL4 1 broad.mit.edu No + MLL4|chr19:40903582-40903582 Missense tccaaCcccca C (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+19 40908522 40908522 TCGA-02-0114 Missense MLL4 1 broad.mit.edu No + MLL4|chr19:40908522-40908522 Missense gcccaGctatc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+19 40916372 40916372 TCGA-02-0010 Missense MLL4 1 broad.mit.edu No + MLL4|chr19:40916372-40916372 Missense cagtgCgtggg C (CpG) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+19 46435815 46435815 TCGA-02-0083 Missense AXL 1 genome.wustl.edu No + AXL|chr19:46435815-46435815 Missense acaccCcttat C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+19 50482763 50482763 TCGA-06-0147 Splice_site MARK4 1 BCM No + MARK4|chr19:50482763-50482763 Other cccccGtgagt G (CpG) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+19 51892838 51892838 TCGA-02-0080 Missense PRKD2 1 broad.mit.edu No - PRKD2|chr19:51892838-51892838 Missense acaagGacacg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+19 52115128 52115128 TCGA-02-0083 Nonsense GRLF1 1 BCM No + GRLF1|chr19:52115128-52115128 Nonsense ccttgGgaaga G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+19 54150026 54150026 TCGA-02-0055 Missense BAX 1 genome.wustl.edu No + BAX|chr19:54150026-54150026 Missense cagagGcgggg G (other) A Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+19 56195600 56195600 TCGA-02-0028 Missense KLK8 1 broad.mit.edu No - KLK8|chr19:56195600-56195600 Missense ccaacCccatt C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 10581166 10581166 TCGA-02-0043 Missense JAG1 1 BCM No - JAG1|chr20:10581166-10581166 Missense tgagcCctggc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 29871752 29871752 TCGA-02-0043 Missense MYLK2 1 broad.mit.edu No + MYLK2|chr20:29871752-29871752 Missense aactaGcagcc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 30361377 30361377 TCGA-02-0083 Missense KIF3B 1 BCM No + KIF3B|chr20:30361377-30361377 Missense agaacCccaaa C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 39177465 39177465 TCGA-02-0083 Missense TOP1 1 genome.wustl.edu No + TOP1|chr20:39177465-39177465 Missense gcagcCcgagg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 56849073 56849073 TCGA-02-0010 Missense GNAS 1 BCM No + GNAS|chr20:56849073-56849073 Missense ccgacGcctcc G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+20 56863479 56863479 TCGA-02-0083 Missense GNAS 1 BCM No + GNAS|chr20:56863479-56863479 Missense ggatgCctccg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+21 45131203 45131203 TCGA-02-0014 Missense ITGB2 1 broad.mit.edu No - ITGB2|chr21:45131203-45131203 Missense gggcaCcgtgg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+21 45144662 45144662 TCGA-06-0158 Splice_site ITGB2 1 broad.mit.edu No - ITGB2|chr21:45144662-45144662 Other aattcGtaagt G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+21 46358384 46358384 TCGA-02-0028 Missense COL6A2 1 genome.wustl.edu No + COL6A2|chr21:46358384-46358384 Missense tgggcCctctg C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 16455484 16455484 TCGA-02-0083 Missense ATP6V1E1 1 broad.mit.edu No - ATP6V1E1|chr22:16455484-16455484 Missense tccggGgagcc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 16590158 16590158 TCGA-02-0083 Missense BCL2L13 1 BCM No + BCL2L13|chr22:16590158-16590158 Missense tgaggGcaagt G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 21853559 21853559 TCGA-02-0083 Missense BCR 1 genome.wustl.edu No + BCR|chr22:21853559-21853559 Missense cagccGcgtcg G (CpG) A Somatic Unknown Somatic Verified OK Use_nonsilent Hypermutated
+22 21926057 21926057 TCGA-02-0102 Missense BCR 1 genome.wustl.edu No + BCR|chr22:21926057-21926057 Missense accaaGatggg G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+22 26476992 26476992 TCGA-02-0028 Missense MN1 1 genome.wustl.edu No - MN1|chr22:26476992-26476992 Missense gtgacGccaag G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 37019247 37019247 TCGA-02-0010 Missense CSNK1E 1 broad.mit.edu No - CSNK1E|chr22:37019247-37019247 Missense atctcGggaag G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 39894533 39894533 TCGA-02-0114 Missense EP300 1 BCM No + EP300|chr22:39894533-39894533 Missense taaaaCcaggc C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+22 39903299 39903299 TCGA-06-0133 Missense EP300 1 BCM No + EP300|chr22:39903299-39903299 Missense cccctCccaat C (TpC) T Somatic Unknown Somatic Verified OK Use_nonsilent Non-hypermutated
+22 39904088 39904088 TCGA-02-0028 Missense EP300 1 BCM No + EP300|chr22:39904088-39904088 Missense agaggGctggc G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+X 20103288 20103288 TCGA-06-0157 Missense RPS6KA3 1 BCM No - RPS6KA3|chrX:20103288-20103288 Missense tcagcTttttc T A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+X 48935116 48935116 TCGA-06-0157 Missense SYP 1 broad.mit.edu No - SYP|chrX:48935116-48935116 Missense ggttcGtgttt G (CpG) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+X 70237836 70237836 TCGA-02-0083 Missense MLLT7 1 genome.wustl.edu No + MLLT7|chrX:70237836-70237836 Missense cagctCccttt C (TpC) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+X 70504111 70504111 TCGA-06-0213 Missense TAF1 1 BCM No + TAF1|chrX:70504111-70504111 Missense tttggGgctgg G (other) A Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+X 70591395 70591395 TCGA-06-0176 Missense TAF1 1 BCM No + TAF1|chrX:70591395-70591395 Missense agaaaGcctgg G (other) C Somatic Valid Somatic Validated OK Use_nonsilent Non-hypermutated
+X 110442569 110442569 TCGA-02-0083 Missense DCX 1 genome.wustl.edu No - DCX|chrX:110442569-110442569 Missense gtctcCcatct C (other) T Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
+X 129111203 129111203 TCGA-02-0114 Missense AIFM1 1 genome.wustl.edu No - AIFM1|chrX:129111203-129111203 Missense aagagGatgaa G (GpA) A Somatic Valid Somatic Validated OK Use_nonsilent Hypermutated
=====================================
test/web/StaticLinkExamples.html
=====================================
@@ -7,6 +7,18 @@
<body>
<h2>IGV desktop links</h2>
+<p>
+ <a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&merge=false&locus=myc">
+ Load merge=false</a>
+</p>
+<p>
+ <a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&merge=true&locus=myc">
+ Load merge=true</a>
+</p>
+<p>
+ <a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&merge=ask&locus=myc">
+ Load merge=ask</a>
+</p>
<p>
<a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&locus=chr1&name=GM12878+loops">
Load with name</a>
@@ -23,6 +35,10 @@
<a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&locus=chr1&name=GM12878+loops;&merge=false">
Load with name into new session</a>
</p>
+<p>
+ <a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.test/data/gm12878_loops.bedpe.gz&locus=chr1&name=GM12878+loops;&merge=true">
+ Load with name into current session</a>
+</p>
<p>
<a href="http://localhost:60151/load?file=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz&index=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz.tbi&locus=chr1&name=SNPs">
Load with index</a>
@@ -43,6 +59,10 @@
<a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.demo/sessions/arcs_session.xml">
Load session</a>
</p>
+<p>
+ <a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.demo/sessions/arcs_session.xml&merge=true">
+ Load session</a>
+</p>
<p>
<a href="http://localhost:60151/load?file=https://s3.amazonaws.com/igv.org.demo/sessions/arcs_session.xml&locus=chr22">
Load session with initial locus (chr22)</a>
@@ -63,6 +83,16 @@
Goto locus 'MYC'</a>
</p>
+<h3>Issue 1261</h3>
+<p>
+ <a href="http://localhost:60151/load?file=https://1000genomes.s3.amazonaws.com/phase3/data/HG01880/alignment/HG01880.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam&merge=ask&locus=chr10%3A89617063">
+ Load HG01880 BAM, merge=ask</a>
+</p>
+<p>
+ <a href="http://localhost:60151/load?file=https://1000genomes.s3.amazonaws.com/phase3/data/HG01879/alignment/HG01879.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam&merge=ask&locus=chr9%3A5443964">
+ Load HG01879 BAM, merge=ask</a>
+</p>
+
<h2>IGV web app links</h2>
<p>
<a target="_blank"
View it on GitLab: https://salsa.debian.org/med-team/igv/-/commit/0d90726e126b4ff6e8cc312c3fea218e7ba74c6e
--
View it on GitLab: https://salsa.debian.org/med-team/igv/-/commit/0d90726e126b4ff6e8cc312c3fea218e7ba74c6e
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