[med-svn] [Git][med-team/vcfanno][upstream] New upstream version 0.3.2
Nilesh Patra
gitlab at salsa.debian.org
Sun Jul 12 20:08:28 BST 2020
Nilesh Patra pushed to branch upstream at Debian Med / vcfanno
Commits:
3229b900 by Nilesh Patra at 2020-07-13T00:14:20+05:30
New upstream version 0.3.2
- - - - -
13 changed files:
- .travis.yml
- + Makefile
- api/api.go
- + tests/by_alt_float/annotation.tsv.gz
- + tests/by_alt_float/annotation.tsv.gz.tbi
- + tests/by_alt_float/conf.toml
- + tests/by_alt_float/q.vcf
- tests/functional-test.sh
- + tests/notbgz/a.conf
- + tests/notbgz/gno.vcf.gz
- + tests/notbgz/gno.vcf.gz.tbi
- + tests/notbgz/notbgz.vcf.gz
- vcfanno.go
Changes:
=====================================
.travis.yml
=====================================
@@ -9,8 +9,10 @@ go:
- 1.8.x
- 1.9.x
- 1.10.x
+ - 1.11.x
before_install:
+ - make
- go get github.com/axw/gocov/gocov
- go get github.com/mattn/goveralls
- if ! go get code.google.com/p/go.tools/cmd/cover; then go get golang.org/x/tools/cmd/cover; fi
=====================================
Makefile
=====================================
@@ -0,0 +1,11 @@
+all: get build
+
+release:
+ CGO_ENABLED=0 GOARCH=amd64 go build -o vcfanno_linux64 --ldflags '-extldflags "-static"' vcfanno.go
+ GOOS=darwin GOARCH=amd64 CGO_ENABLED=0 go build -o vcfanno_osx --ldflags '-extldflags "-static"' vcfanno.go
+
+get:
+ go get -t ./...
+
+build:
+ go build -o vcfanno vcfanno.go
=====================================
api/api.go
=====================================
@@ -540,6 +540,13 @@ func (s *Source) UpdateHeader(r HeaderUpdater, ends bool, htype string, number s
if s.Op == "by_alt" {
number = "A"
ntype = "String"
+ if strings.HasSuffix(s.Name, "_float") {
+ ntype = "Float"
+ s.Name = s.Name[:len(s.Name)-6]
+ } else if strings.HasSuffix(s.Name, "_int") {
+ ntype = "Integer"
+ s.Name = s.Name[:len(s.Name)-4]
+ }
// for 'self' and 'first', we can get the type from the header of the annotation file.
} else if htype != "" && (s.Op == "self" || s.Op == "first") {
ntype = htype
=====================================
tests/by_alt_float/annotation.tsv.gz
=====================================
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=====================================
tests/by_alt_float/annotation.tsv.gz.tbi
=====================================
Binary files /dev/null and b/tests/by_alt_float/annotation.tsv.gz.tbi differ
=====================================
tests/by_alt_float/conf.toml
=====================================
@@ -0,0 +1,5 @@
+[[annotation]]
+names = ["CADD_RAW_float"]
+file = "annotation.tsv.gz"
+columns = [5]
+ops = ["by_alt"]
=====================================
tests/by_alt_float/q.vcf
=====================================
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##contig=<ID=chr2,length=242193529,assembly=GRCh38>
+##INFO=<ID=AF,Number=.,Type=Float,Description="">
+##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
+##hailversion=0.2.9-8588a25687af
+#CHROM POS ID REF ALT QUAL FILTER INFO
+chr2 41647 2_41647_A_G A G 1328.0 . AF=1.56250e-02;AQ=1328
=====================================
tests/functional-test.sh
=====================================
@@ -56,6 +56,9 @@ names=["nef"]
fields=["xxx"]
EOF
+run check_not_bgz vcfanno -p 4 tests/notbgz/a.conf tests/notbgz/notbgz.vcf.gz
+assert exit_code 0
+
run check_field_warning vcfanno -lua example/custom.lua __t.conf example/exac.vcf.gz
assert_exit_code 0
assert_in_stderr "xxx not found in header"
@@ -184,3 +187,10 @@ run self_test_with_A_and_many_overlaps fn_self_test_with_A_and_many_overlaps
assert_exit_code 0
assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AC=35,65;GN_AF=0.3717,0.6122"
assert_in_stdout "ID=GN_AF,Number=A"
+
+
+run check_by_alts_float vcfanno -base-path tests/by_alt_float/ tests/by_alt_float/conf.toml tests/by_alt_float/q.vcf
+assert_exit_code 0
+assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AF=1.56250e-02;AQ=1328;CADD_RAW=0.591814"
+go install -a
+
=====================================
tests/notbgz/a.conf
=====================================
@@ -0,0 +1,5 @@
+[[annotation]]
+file="tests/notbgz/gno.vcf.gz"
+fields = ["AF", "AF_AFR", "AF_AMR", "AF_ASJ", "AF_FIN", "AF_NFE", "AF_OTH", "AF_SAS"]
+names = ["gnomad_AF", "gnomad_AF_AFR", "gnomad_AF_AMR", "gnomad_AF_ASJ", "gnomad_AF_FIN", "gnomad_AF_NFE", "gnomad_AF_OTH", "gnomad_AF_SAS"]
+ops=["max", "max", "max", "max", "max", "max", "max", "max"]
=====================================
tests/notbgz/gno.vcf.gz
=====================================
Binary files /dev/null and b/tests/notbgz/gno.vcf.gz differ
=====================================
tests/notbgz/gno.vcf.gz.tbi
=====================================
Binary files /dev/null and b/tests/notbgz/gno.vcf.gz.tbi differ
=====================================
tests/notbgz/notbgz.vcf.gz
=====================================
@@ -0,0 +1,300 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=FS,Description="FS > 30.0">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=QD,Description="QD < 2.0">
+##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=MMQ,Number=A,Type=Integer,Description="median mapping quality">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path 27571P-1_0_249250621_genomicsdb --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/variation/rnaseq/gatk-haplotype/Sample_1__27571P-gatk-haplotype.vcf.gz --reader-threads 1 --intervals 1:1-249250621 --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --batch-size 0 --consolidate false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.6.0,Date="August 6, 2018 9:18:13 PM EDT">
+##GATKCommandLine=<ID=GenotypeGVCFs,CommandLine="GenotypeGVCFs --output /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/bcbiotx/tmpCs8vG6/27571P-1_0_249250621.vcf.gz --use-new-qual-calculator true --variant gendb:///mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/joint/gatk-haplotype-joint/27571P/1/27571P-1_0_249250621_genomicsdb --intervals 1:1-249250621 --reference /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --only-output-calls-starting-in-intervals false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.6.0,Date="August 6, 2018 9:20:32 PM EDT">
+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --emit-ref-confidence GVCF --gvcf-gq-bands 10 --gvcf-gq-bands 20 --gvcf-gq-bands 30 --gvcf-gq-bands 40 --gvcf-gq-bands 60 --gvcf-gq-bands 80 --native-pair-hmm-threads 1 --output /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/bcbiotx/tmp7bfK6h/Sample_1__27571P-1_0_62094793-gatk-haplotype.vcf.gz --intervals /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/variation/rnaseq/gatk-haplotype/regions/Sample_1__27571P-1_0_62094793-gatk-haplotype-regions.bed --interval-set-rule INTERSECTION --input /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/align/Sample_1__27571P/Sample_1__27571P-dedup.splitN.bam --reference /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --annotation ClippingRankSumTest --annotation DepthPerSampleHC --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.6.0,Date="August 5, 2018 8:56:28 PM EDT">
+##GATKCommandLine=<ID=VariantFiltration,CommandLine="VariantFiltration --output /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/bcbiotx/tmpHjZiKO/27571P-joint-annotated-rnaedit-filter.vcf.gz --filter-expression FS > 30.0 --filter-expression QD < 2.0 --filter-name FS --filter-name QD --cluster-size 3 --cluster-window-size 35 --variant /mnt/isilon/cbmi/variome/rathik/mendelian_rnaseq/gatk_output/27571P/joint/gatk-haplotype-joint/27571P/27571P-joint-annotated-rnaedit.vcf.gz --reference /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.6.0,Date="August 6, 2018 10:20:28 PM EDT">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score >From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=possible_rnaedit,Number=0,Type=Flag,Description="calculated by lua:is_edit_flag(ref, alt) of overlapping values in column 4 from /mnt/isilon/cbmi/variome/bin/bcbio-nextgen/bcbio/genomes/Hsapiens/GRCh37/editing/RADAR.bed.gz">
+##contig=<ID=1,length=249250621>
+##contig=<ID=2,length=243199373>
+##contig=<ID=3,length=198022430>
+##contig=<ID=4,length=191154276>
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+##contig=<ID=GL000236.1,length=41934>
+##contig=<ID=GL000241.1,length=42152>
+##contig=<ID=GL000243.1,length=43341>
+##contig=<ID=GL000242.1,length=43523>
+##contig=<ID=GL000230.1,length=43691>
+##contig=<ID=GL000237.1,length=45867>
+##contig=<ID=GL000233.1,length=45941>
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+##contig=<ID=GL000220.1,length=161802>
+##contig=<ID=GL000213.1,length=164239>
+##contig=<ID=GL000211.1,length=166566>
+##contig=<ID=GL000199.1,length=169874>
+##contig=<ID=GL000217.1,length=172149>
+##contig=<ID=GL000216.1,length=172294>
+##contig=<ID=GL000215.1,length=172545>
+##contig=<ID=GL000205.1,length=174588>
+##contig=<ID=GL000219.1,length=179198>
+##contig=<ID=GL000224.1,length=179693>
+##contig=<ID=GL000223.1,length=180455>
+##contig=<ID=GL000195.1,length=182896>
+##contig=<ID=GL000212.1,length=186858>
+##contig=<ID=GL000222.1,length=186861>
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+##contig=<ID=GL000225.1,length=211173>
+##contig=<ID=GL000192.1,length=547496>
+##source=GenomicsDBImport
+##source=GenotypeGVCFs
+##source=HaplotypeCaller
+##source=VariantFiltration
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR
+1 14522 . G A 142.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.47;ClippingRankSum=0.00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=15.84;ReadPosRankSum=1.20;SOR=0.527 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:5,4:9:99:60,0:0|1:14522_G_A:150,0,240
+1 14542 . A G 214.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;ClippingRankSum=0.00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=13.41;ReadPosRankSum=0.490;SOR=1.085 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:10,6:16:99:60,0:0|1:14522_G_A:222,0,382
+1 14574 . A G 677.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-9.280e-01;ClippingRankSum=0.00;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=16.53;ReadPosRankSum=-8.940e-01;SOR=1.316 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:23,18:41:99:60,0:0|1:14574_A_G:685,0,912
+1 14590 . G A 571.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;ClippingRankSum=0.00;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=12.16;ReadPosRankSum=2.24;SOR=0.790 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:31,16:47:99:60,0:0|1:14574_A_G:579,0,1254
+1 14599 . T A 561.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-9.360e-01;ClippingRankSum=0.00;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=11.46;ReadPosRankSum=3.23;SOR=0.723 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:33,16:49:99:60,0:0|1:14574_A_G:569,0,1379
+1 14604 . A G 558.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=1.50;ClippingRankSum=0.00;DP=51;ExcessHet=3.0103;FS=2.653;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=10.95;ReadPosRankSum=3.04;SOR=1.657 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:35,16:51:99:60,0:0|1:14574_A_G:566,0,1421
+1 14610 . T C 636.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=1.24;ClippingRankSum=0.00;DP=55;ExcessHet=3.0103;FS=5.359;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=11.57;ReadPosRankSum=1.53;SOR=2.176 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:37,18:55:99:60,0:0|1:14574_A_G:644,0,1479
+1 14653 . C T 2517.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.65;ClippingRankSum=0.00;DP=133;ExcessHet=3.0103;FS=23.228;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=18.93;ReadPosRankSum=-1.537e+00;SOR=3.383 GT:AD:DP:GQ:MMQ:PL 0/1:68,65:133:99:60,0:2525,0,2295
+1 14907 . A G 428.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.030e+00;ClippingRankSum=0.00;DP=72;ExcessHet=3.0103;FS=17.057;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=5.95;ReadPosRankSum=5.14;SOR=0.034 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:58,14:72:99:60,0:0|1:14907_A_G:436,0,2304
+1 14930 . A G 545.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-9.000e-03;ClippingRankSum=0.00;DP=79;ExcessHet=3.0103;FS=23.790;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.91;ReadPosRankSum=5.49;SOR=0.025 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:61,18:79:99:60,0:0|1:14907_A_G:553,0,2401
+1 15015 . G C 218.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.985;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=2.586;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.81;SOR=1.345 GT:AD:DP:GQ:MMQ:PL 0/1:21,7:28:99:60,0:226,0,739
+1 15208 . G A 163.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.930e-01;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.79;ReadPosRankSum=-9.360e-01;SOR=0.368 GT:AD:DP:GQ:MMQ:PL 0/1:14,7:21:99:60,0:171,0,481
+1 15211 . T G 613.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.370e-01;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=29.22;ReadPosRankSum=-1.441e+00;SOR=1.085 GT:AD:DP:GQ:MMQ:PL 0/1:4,17:21:76:60,0:621,0,76
+1 15274 . A G,T 487 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=25.36;SOR=2.670 GT:AD:DP:GQ:MMQ:PL 1/2:0,2,10:12:54:60,60,0:504,420,414,84,0,54
+1 16257 . G C 38.60 QD AC=1;AF=0.500;AN=2;BaseQRankSum=0.040;ClippingRankSum=0.00;DP=46;ExcessHet=3.0103;FS=1.887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=0.84;ReadPosRankSum=-1.098e+00;SOR=0.877 GT:AD:DP:GQ:MMQ:PL 0/1:41,5:46:46:60,0:46,0,1301
+1 16288 . C G 154.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.862;ClippingRankSum=0.00;DP=36;ExcessHet=3.0103;FS=7.396;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=4.29;ReadPosRankSum=0.553;SOR=2.280 GT:AD:DP:GQ:MMQ:PL 0/1:30,6:36:99:60,0:162,0,1221
+1 16298 . C T 256.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.62;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=10.268;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=8.28;ReadPosRankSum=0.166;SOR=2.564 GT:AD:DP:GQ:MMQ:PL 0/1:24,7:31:99:60,0:264,0,900
+1 16378 . T C 676.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.888e+00;ClippingRankSum=0.00;DP=48;ExcessHet=3.0103;FS=20.750;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=14.10;ReadPosRankSum=2.00;SOR=1.812 GT:AD:DP:GQ:MMQ:PL 0/1:26,22:48:99:60,0:684,0,945
+1 16495 . G C 415.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;ClippingRankSum=0.00;DP=61;ExcessHet=3.0103;FS=1.076;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.81;ReadPosRankSum=-1.506e+00;SOR=0.457 GT:AD:DP:GQ:MMQ:PL 0/1:42,19:61:99:60,0:423,0,1463
+1 16497 . A G 424.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-8.880e-01;ClippingRankSum=0.00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.08;ReadPosRankSum=-8.870e-01;SOR=0.776 GT:AD:DP:GQ:MMQ:PL 0/1:40,20:60:99:60,0:432,0,1413
+1 16534 . C T 469.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.667;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=4.029;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=12.04;ReadPosRankSum=0.174;SOR=0.174 GT:AD:DP:GQ:MMQ:PL 0/1:24,15:39:99:60,0:477,0,841
+1 16571 . G A 241.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.679;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=10.98;ReadPosRankSum=-1.303e+00;SOR=0.223 GT:AD:DP:GQ:MMQ:PL 0/1:15,7:22:99:60,0:249,0,609
+1 16580 . C G 67.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.56;ReadPosRankSum=-9.460e-01;SOR=0.054 GT:AD:DP:GQ:MMQ:PL 0/1:16,3:19:75:60,0:75,0,705
+1 16949 . A C 130.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=10.05;ReadPosRankSum=0.447;SOR=0.223 GT:AD:DP:GQ:MMQ:PL 0/1:9,4:13:99:60,0:138,0,409
+1 16974 . C T 31.60 QD AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=1.86;ReadPosRankSum=0.373;SOR=0.035 GT:AD:DP:GQ:MMQ:PL 0/1:15,2:17:39:60,0:39,0,625
+1 16996 . T C 76.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=4.51;ReadPosRankSum=-7.590e-01;SOR=0.069 GT:AD:DP:GQ:MMQ:PL 0/1:14,3:17:84:60,0:84,0,559
+1 17055 . C CAGGTT 28.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=9.55;ReadPosRankSum=-9.670e-01;SOR=0.368 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,1:3:36:60,0:0|1:17055_C_CAGGTT:36,0,77
+1 17056 . C CTCGG 28.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=9.55;ReadPosRankSum=-9.670e-01;SOR=0.368 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,1:3:36:60,0:0|1:17055_C_CAGGTT:36,0,77
+1 17407 . G A 209.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.730e-01;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=11.03;ReadPosRankSum=-5.720e-01;SOR=0.804 GT:AD:DP:GQ:MMQ:PL 0/1:12,7:19:99:60,0:217,0,606
+1 17538 . C A 64.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.08;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=6.067;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.08;ReadPosRankSum=-9.910e-01;SOR=0.889 GT:AD:DP:GQ:MMQ:PL 0/1:18,3:21:72:60,0:72,0,933
+1 18062 . C CT 256 PASS AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.73;SOR=1.329 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,6:6:18:60,0:1|1:18062_C_CT:270,18,0
+1 18064 . G GATGGCCTTCTTGCTGCCCTTGATCTTCTCAATCTTGGCC 256 PASS AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.97;SOR=1.329 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,6:6:18:60,0:1|1:18062_C_CT:270,18,0
+1 19226 . T A 205.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;ClippingRankSum=0.00;DP=34;ExcessHet=3.0103;FS=5.146;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.05;ReadPosRankSum=-6.030e-01;SOR=2.012 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:27,7:34:99:60,0:0|1:19226_T_A:213,0,5280
+1 19249 . G A 235.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;ClippingRankSum=0.00;DP=38;ExcessHet=3.0103;FS=7.857;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.20;ReadPosRankSum=0.900;SOR=2.595 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:30,8:38:99:60,0:0|1:19226_T_A:243,0,5947
+1 19254 . G C 235.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=7.954;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.04;ReadPosRankSum=0.943;SOR=2.792 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:31,8:39:99:60,0:0|1:19226_T_A:243,0,5947
+1 19279 . C T 275.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-3.500e-01;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=5.808;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.07;ReadPosRankSum=-4.280e-01;SOR=1.961 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:29,10:39:99:60,0:0|1:19226_T_A:283,0,5479
+1 19322 . C T 232.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.607;ClippingRankSum=0.00;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=9.30;ReadPosRankSum=-3.240e-01;SOR=0.569 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:18,7:25:99:60,0:0|1:19322_C_T:240,0,866
+1 19355 . G A 244.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.120e-01;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=11.65;ReadPosRankSum=-2.250e-01;SOR=0.250 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:14,7:21:99:60,0:1|0:19322_C_T:252,0,837
+1 19391 . G A 55.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.480e+00;ClippingRankSum=0.00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.18;ReadPosRankSum=0.140;SOR=0.132 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:7,2:9:63:60,0:1|0:19322_C_T:63,0,475
+1 20037 . A C 88.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.730;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.82;ReadPosRankSum=0.290;SOR=0.495 GT:AD:DP:GQ:MMQ:PL 0/1:10,3:13:96:60,0:96,0,576
+1 20129 . C T 190.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080e-01;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.94;ReadPosRankSum=1.15;SOR=0.591 GT:AD:DP:GQ:MMQ:PL 0/1:18,6:24:99:60,0:198,0,757
+1 20184 . A G 245.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-8.000e-02;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=7.384;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=11.16;ReadPosRankSum=-7.540e-01;SOR=1.759 GT:AD:DP:GQ:MMQ:PL 0/1:14,8:22:99:60,0:253,0,526
+1 20221 . G C 31.60 QD AC=1;AF=0.500;AN=2;BaseQRankSum=-2.907e+00;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=1.86;ReadPosRankSum=1.25;SOR=0.582 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:15,2:17:39:60,0:0|1:20221_G_C:39,0,633
+1 20227 . T C 34.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.149e+00;ClippingRankSum=0.00;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=2.16;ReadPosRankSum=0.815;SOR=0.473 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:14,2:16:42:60,0:0|1:20221_G_C:42,0,582
+1 24832 . A G 43.60 QD AC=1;AF=0.500;AN=2;BaseQRankSum=-8.910e-01;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=9.700;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=1.56;ReadPosRankSum=0.692;SOR=0.003 GT:AD:DP:GQ:MMQ:PL 0/1:25,3:28:51:60,0:51,0,1518
+1 127573 . G A 187.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.22;ClippingRankSum=0.00;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=18.76;ReadPosRankSum=0.674;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 0/1:5,5:10:99:60,0:195,0,214
+1 135040 . T C 1172.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.06;ClippingRankSum=0.00;DP=65;ExcessHet=3.0103;FS=2.115;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=18.04;ReadPosRankSum=0.678;SOR=0.452 GT:AD:DP:GQ:MMQ:PL 0/1:29,36:65:99:60,0:1180,0,1200
+1 135982 . A G 255.90 PASS AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.24;SOR=3.912 GT:AD:DP:GQ:MMQ:PL 1/1:0,6:6:18:60,0:270,18,0
+1 136048 . C T 175.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.18;ClippingRankSum=0.00;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=5.49;ReadPosRankSum=0.545;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 0/1:24,8:32:99:60,0:183,0,639
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+1 568419 . T C 436 PASS AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.23;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,10:10:30:60,0:1|1:568419_T_C:450,30,0
+1 568442 . T C 836 PASS AC=2;AF=1.00;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.03;SOR=0.793 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,19:19:60:60,0:1|1:568419_T_C:850,60,0
+1 568463 . A G 984 PASS AC=2;AF=1.00;AN=2;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.67;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,26:26:78:60,0:1|1:568419_T_C:998,78,0
+1 568572 . G A 184 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.00;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 1/1:0,8:8:24:60,0:198,24,0
+1 568616 . A G 481 PASS AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.05;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 1/1:0,20:20:60:60,0:495,60,0
+1 568691 . T C 78.30 SnpCluster AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=26.61;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,2:2:6:60,0:1|1:568691_T_C:90,6,0
+1 568703 . A G 78.30 SnpCluster AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=29.20;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,2:2:6:60,0:1|1:568691_T_C:90,6,0
+1 568718 . C T 78.30 SnpCluster AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=28.55;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,2:2:6:60,0:1|1:568691_T_C:90,6,0
+1 568752 . T C 37.30 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=18.64;SOR=2.303 GT:AD:DP:GQ:MMQ:PL 1/1:0,2:2:6:60,0:49,6,0
+1 569004 . T C 931 PASS AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.42;SOR=0.990 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,21:21:63:60,0:1|1:569004_T_C:945,63,0
+1 569010 . T C 931 PASS AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.53;SOR=0.990 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,21:21:63:60,0:1|1:569004_T_C:945,63,0
+1 569052 . C T 546 PASS AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.00;SOR=0.784 GT:AD:DP:GQ:MMQ:PL 1/1:0,21:21:63:60,0:560,63,0
+1 569094 . A G 976 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.23;SOR=1.179 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,3:3:66:60,0:1|1:569094_A_G:990,66,0
+1 569106 . G A 3541 PASS AC=2;AF=1.00;AN=2;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.52;SOR=6.518 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,79:79:99:60,0:1|1:569094_A_G:3555,238,0
+1 569204 . T C 620.10 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-5.340e-01;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=3.245;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=32.64;ReadPosRankSum=0.462;SOR=0.556 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:1,18:19:12:60,0:1|1:569204_T_C:634,12,0
+1 569226 . C A 490 PASS AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.47;SOR=0.892 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,9:9:39:60,0:1|1:569204_T_C:504,39,0
+1 569250 . G A 616 PASS AC=2;AF=1.00;AN=2;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.91;SOR=2.985 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,14:14:42:60,0:1|1:569204_T_C:630,42,0
+1 569267 . G A 626.30 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.34;ClippingRankSum=0.00;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=31.31;ReadPosRankSum=1.28;SOR=2.584 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:1,14:15:6:60,0:1|1:569204_T_C:638,6,0
+1 569301 . A G 46790 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-5.340e-01;ClippingRankSum=0.00;DP=1046;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=31.45;ReadPosRankSum=0.352;SOR=8.480 GT:AD:DP:GQ:MMQ:PL 1/1:2,1044:1046:99:60,0:46804,3059,0
+1 569492 . T C 23316 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=3.43;ClippingRankSum=0.00;DP=573;ExcessHet=3.0103;FS=13.011;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=33.27;ReadPosRankSum=-4.598e+00;SOR=7.197 GT:AD:DP:GQ:MMQ:PL 1/1:8,561:569:99:60,0:23330,1449,0
+1 569609 . A C 1053.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.177e+00;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=5.576;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=33.99;ReadPosRankSum=2.29;SOR=0.102 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:4,27:31:81:60,0:0|1:569609_A_C:1061,0,81
+1 569624 . T C 1232 PASS AC=2;AF=1.00;AN=2;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.26;SOR=1.460 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,29:29:51:60,0:1|1:569609_A_C:1246,51,0
+1 569717 . T C 197.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.080e-01;ClippingRankSum=0.00;DP=9;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=21.96;ReadPosRankSum=-2.100e-01;SOR=0.515 GT:AD:DP:GQ:MMQ:PL 0/1:2,7:9:62:60,0:205,0,62
+1 569803 . G A 412.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-7.140e-01;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=18.75;ReadPosRankSum=-1.300e-01;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 0/1:4,18:22:73:60,0:420,0,73
+1 569809 . A G 16.60 QD;SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=0.75;ReadPosRankSum=-2.266e+00;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:20,2:22:24:60,0:0|1:569809_A_G:24,0,834
+1 569810 . A T 16.60 QD;SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=1.72;ClippingRankSum=0.00;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=0.75;ReadPosRankSum=-2.264e+00;SOR=0.693 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:20,2:22:24:60,0:0|1:569809_A_G:24,0,834
+1 569811 . C T 16.60 QD;SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=2.71;ClippingRankSum=0.00;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=0.79;ReadPosRankSum=-1.611e+00;SOR=1.609 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:20,1:21:24:60,0:0|1:569809_A_G:24,0,834
+1 569874 . C T 796 PASS AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.76;SOR=0.914 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,18:18:54:60,0:1|1:569874_C_T:810,54,0
+1 569878 . C G 796 PASS AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.09;SOR=0.914 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,18:18:54:60,0:1|1:569874_C_T:810,54,0
+1 569983 . G A 354.30 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.665;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=20.84;ReadPosRankSum=-1.510e-01;SOR=0.818 GT:AD:DP:GQ:MMQ:PL 1/1:2,15:17:6:60,0:366,6,0
+1 570076 . T C 469.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-3.455e+00;ClippingRankSum=0.00;DP=14;ExcessHet=3.0103;FS=3.256;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=33.54;ReadPosRankSum=2.32;SOR=0.105 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,12:14:48:60,0:0|1:570076_T_C:477,0,48
+1 570079 . C T 469.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-2.810e+00;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=3.123;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=26.08;ReadPosRankSum=2.29;SOR=0.141 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,11:13:48:60,0:0|1:570076_T_C:477,0,48
+1 570089 . C T 406.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-3.151e+00;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=3.282;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=33.88;ReadPosRankSum=2.28;SOR=0.105 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,10:12:54:60,0:0|1:570076_T_C:414,0,54
+1 570094 . G A 406.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-2.287e+00;ClippingRankSum=0.00;DP=10;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=33.85;ReadPosRankSum=2.29;SOR=0.105 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,8:10:54:60,0:0|1:570076_T_C:414,0,54
+1 570097 . A G 322.60 SnpCluster AC=1;AF=0.500;AN=2;BaseQRankSum=-2.287e+00;ClippingRankSum=0.00;DP=10;ExcessHet=3.0103;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=32.26;ReadPosRankSum=2.29;SOR=0.105 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:2,8:10:60:60,0:0|1:570076_T_C:330,0,60
+1 570178 . G A 708.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.387e+00;ClippingRankSum=0.00;DP=37;ExcessHet=3.0103;FS=3.928;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=19.15;ReadPosRankSum=-3.310e-01;SOR=0.588 GT:AD:DP:GQ:MMQ:PL 0/1:6,31:37:78:60,0:716,0,78
+1 645624 . A AT 45.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=15.21;ReadPosRankSum=0.00;SOR=0.223 GT:AD:DP:GQ:MMQ:PL 0/1:1,2:3:22:60,0:53,0,22
+1 652753 . A AAT 69.30 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=34.66;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 1/1:0,2:2:6:60,0:81,6,0
+1 662029 . G A 2101 PASS AC=2;AF=1.00;AN=2;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.08;SOR=7.743 GT:AD:DP:GQ:MMQ:PL 1/1:0,47:47:99:60,0:2115,141,0
+1 662313 . T C 25.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.190e-01;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=6.40;ReadPosRankSum=-6.740e-01;SOR=1.022 GT:AD:DP:GQ:MMQ:PL 0/1:3,1:4:33:60,0:33,0,123
+1 662353 . T C 115.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.190e-01;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=28.90;ReadPosRankSum=0.00;SOR=0.446 GT:AD:DP:GQ:MMQ:PL 0/1:1,3:4:33:60,0:123,0,33
+1 662584 . T C 92.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.217e+00;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.12;ReadPosRankSum=-7.180e-01;SOR=0.836 GT:AD:DP:GQ:MMQ:PL 0/1:9,4:13:99:60,0:100,0,470
+1 662647 . T C 260.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.590e-01;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=21.72;ReadPosRankSum=-8.750e-01;SOR=0.634 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:3,9:12:99:60,0:0|1:662641_T_C:268,0,103
+1 663097 . G C 80.80 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;QD=26.93;SOR=1.179 GT:AD:DP:GQ:MMQ:PL 1/1:0,3:3:9:60,0:94,9,0
+1 679604 . C A 166.10 PASS AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.42;SOR=3.258 GT:AD:DP:GQ:MMQ:PL 1/1:0,4:4:12:60,0:180,12,0
+1 680144 . A C 73.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=24.53;ReadPosRankSum=-4.310e-01;SOR=1.179 GT:AD:DP:GQ:MMQ:PL 0/1:1,2:3:49:60,0:81,0,49
+1 680246 . G A 73.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=24.53;ReadPosRankSum=0.967;SOR=2.225 GT:AD:DP:GQ:MMQ:PL 0/1:1,2:3:40:60,0:81,0,40
+1 684766 . A AT 300 PASS AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.65;SOR=1.609 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,7:7:21:60,0:1|1:684766_A_AT:314,21,0
+1 684767 . A AACATGTTGCCCAGTCAGTTTCTCTTCCTGGATTC 301 PASS AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.48;SOR=1.609 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,7:7:21:60,0:1|1:684766_A_AT:315,21,0
+1 700565 . C G 12.60 QD AC=1;AF=0.500;AN=2;BaseQRankSum=-7.280e-01;ClippingRankSum=0.00;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=1.26;ReadPosRankSum=-4.310e-01;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 0/1:8,2:10:20:60,0:20,0,306
+1 703993 . T TTCGGATC 346 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.56;SOR=4.407 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,8:8:24:60,0:1|1:703993_T_TTCGGATC:360,24,0
+1 703995 . T TTGTAAGAGCAGAGCAGGTGATGGAGAGGGTGGGAGGTGTAGTGACAGAAGCAGGAAACTCCAGTCATTCGAGACG 346 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.63;SOR=4.407 GT:AD:DP:GQ:MMQ:PGT:PID:PL 1/1:0,8:8:24:60,0:1|1:703993_T_TTCGGATC:360,24,0
+1 708461 . G T 526.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.460e-01;ClippingRankSum=0.00;DP=14;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=30.55;ReadPosRankSum=-9.040e-01;SOR=0.916 GT:AD:DP:GQ:MMQ:PL 0/1:1,13:14:22:60,0:534,0,22
+1 713786 . G GGCT 542.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.505e+00;ClippingRankSum=0.00;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=21.71;ReadPosRankSum=1.17;SOR=0.551 GT:AD:DP:GQ:MMQ:PL 0/1:12,13:25:99:60,0:550,0,462
+1 713914 . A G 73.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.49;ClippingRankSum=0.00;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=4.09;ReadPosRankSum=0.912;SOR=0.551 GT:AD:DP:GQ:MMQ:PL 0/1:15,3:18:81:60,0:81,0,694
+1 713931 . A G 76.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.57;ClippingRankSum=0.00;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=4.51;ReadPosRankSum=-1.930e-01;SOR=0.283 GT:AD:DP:GQ:MMQ:PL 0/1:14,3:17:84:60,0:84,0,696
+1 713954 . T C 43.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.41;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.35;ReadPosRankSum=-9.660e-01;SOR=0.260 GT:AD:DP:GQ:MMQ:PL 0/1:11,2:13:51:60,0:51,0,532
+1 714427 . G A 346 PASS AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.62;SOR=0.892 GT:AD:DP:GQ:MMQ:PL 1/1:0,9:9:27:60,0:360,27,0
+1 714471 . G GGCAGAA 19.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.210;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.27;ReadPosRankSum=-9.670e-01;SOR=1.518 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:5,1:6:27:60,0:0|1:714471_G_GGCAGAA:27,0,207
+1 714476 . C A 19.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.27;ReadPosRankSum=-1.383e+00;SOR=1.518 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:5,1:6:27:60,0:0|1:714471_G_GGCAGAA:27,0,207
+1 714477 . G GCATGAGCAAATTACTTTTTAGAGGTAACTT 19.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.210;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.27;ReadPosRankSum=-1.383e+00;SOR=1.518 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:5,1:6:27:60,0:0|1:714471_G_GGCAGAA:27,0,207
+1 714480 . C CTGAACTTGT 19.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.431;ClippingRankSum=0.00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=3.27;ReadPosRankSum=-1.383e+00;SOR=1.518 GT:AD:DP:GQ:MMQ:PGT:PID:PL 0/1:5,1:6:27:60,0:0|1:714471_G_GGCAGAA:27,0,207
+1 715348 . T G 120.10 PASS AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.02;SOR=1.609 GT:AD:DP:GQ:MMQ:PL 1/1:0,4:4:12:60,0:134,12,0
+1 715762 . A G 29.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=7.40;ReadPosRankSum=0.00;SOR=0.105 GT:AD:DP:GQ:MMQ:PL 0/1:2,2:4:37:60,0:37,0,117
+1 716421 . A G 17.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.242e+00;ClippingRankSum=0.00;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.00;QD=2.20;ReadPosRankSum=-8.540e-01;SOR=0.693 GT:AD:DP:GQ:MMQ:PL 0/1:6,2:8:25:60,0:25,0,284
+1 718555 . T C 210.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.33;SOR=3.611 GT:AD:DP:GQ:MMQ:PL 1/1:0,5:5:15:60,0:225,15,0
=====================================
vcfanno.go
=====================================
@@ -25,7 +25,7 @@ import (
"github.com/brentp/xopen"
)
-var VERSION = "0.3.1"
+var VERSION = "0.3.2"
func envGet(name string, vdefault int) int {
sval := os.Getenv(name)
@@ -128,25 +128,32 @@ see: https://github.com/brentp/vcfanno
var err error
var qrdr io.Reader
- // try to parallelizing reading if we have plenty of CPUs and it's (possibly)
+ // try to parallelize reading if we have plenty of CPUs and it's (possibly)
// a bgzf file.
- if len(config.Annotation) < runtime.GOMAXPROCS(0) && strings.HasSuffix(queryFile, ".gz") {
+ if len(config.Annotation) < runtime.GOMAXPROCS(0) && strings.HasSuffix(queryFile, ".gz") || strings.HasSuffix(queryFile, ".bgz") {
if rdr, err := os.Open(queryFile); err == nil {
if st, err := rdr.Stat(); err == nil && st.Size() > 2320303098 {
qrdr, err = bgzf.NewReader(rdr, 4)
if err == nil {
- log.Printf("using 4 worker threads to decompress query file")
+ log.Printf("using 4 worker threads to decompress bgzip file")
+ } else {
+ qrdr = nil
}
} else {
qrdr, err = bgzf.NewReader(rdr, 2)
if err == nil {
- log.Printf("using 2 worker threads to decompress query file")
+ log.Printf("using 2 worker threads to decompress bgzip file")
+ } else {
+ qrdr = nil
}
}
+ } else {
+ log.Fatal(err)
}
}
if qrdr == nil {
qrdr, err = xopen.Ropen(queryFile)
+ log.Printf("falling back to non-bgzip")
}
if err != nil {
log.Fatal(fmt.Errorf("error opening query file %s: %s", queryFile, err))
View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/commit/3229b900ea3cbe4d5a3f65340ace2ba1b4bdfaab
--
View it on GitLab: https://salsa.debian.org/med-team/vcfanno/-/commit/3229b900ea3cbe4d5a3f65340ace2ba1b4bdfaab
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