[med-svn] [varscan] 01/01: Add upstream release notes

[Andreas Tille]

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tille pushed a commit to branch master
in repository varscan.

commit 2463a5b2a106a9e82e1ddaa3d312fc8b09e82062
Author: Andreas Tille <tille at debian.org>
Date:   Thu Apr 17 11:20:18 2014 +0200

    Add upstream release notes
---
 debian/release-notes.txt | 66 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/rules             |  3 +++
 2 files changed, 69 insertions(+)

diff --git a/debian/release-notes.txt b/debian/release-notes.txt
new file mode 100644
index 0000000..8e3a51e
--- /dev/null
+++ b/debian/release-notes.txt
@@ -0,0 +1,66 @@
+RELEASE NOTES FOR VARSCAN V2.3.6
+
+29-July-2013
+
+VarScan v2.3.6 includes these bug fixes:
+-Corrected VCF output format for deletions, which had a bug
+-For somatic, fixed a bug so that --strand-filter can be set to 0 or 1.
+-Fixed an issue with mpileup2cns where it crashed at the strange SAMtools mpileup lines with 0x depth.
+-Turned off a debugging message concerning indels ("failed with A+").
+-Added VCF compatibility for the filtering commands
+
+MORE VCF COMPATIBILITY
+The following commands are now compatible with VCF files:
+processSomatic
+filter
+somaticFilter
+
+NEW FEATURE: TRIO CALLING
+A method for trio calling is now available with the subcommand "trio". We have used it internally, but this is the first external release 
+of the code, so I'd consider it a "beta" feature. Your feedback is welcome!
+
+Usage:
+java -jar VarScan.jar trio [fatherMotherChild.mpileup] [varScan.output] 
+
+Your input file [fatherMotherChild.mpileup] should be a SAMtools mpileup file with father, mother, and child data, in that order. 
+
+The [varScan.output] is a basename for your output VCFs. VCF is the only output format option.
+
+If you provide piped input, you must use the --output-name parameter to specify a basename for output files.
+
+Output:
+Two VCFs, one for SNPs and one for indels, e.g. varScan.output.snp.vcf and varScan.output.indel.vcf
+
+Methods:
+This feature employs some special methodology to aid family studies:
+
+1.) Detection of de novo mutations. The underlying assumptions are that the parents truly are the biological parents, and that true de novo mutations are rare. 
+We define a de novo mutation as a variant present in the child but absent from both parents. Other differences, such as two homozygous-variant parents and a wild-type child, are classified as MIE (Mendelian Inheritance Error).
+Candidate de novos (mother=0/0 father=0/0 child!=0/0) are re-called using a separate set of user-defined parameters (see usage) to detect under-sampled variants in either parent.
+
+2.) Trio status. Other trio statuses (transmitted, untransmitted, or Mendelian inheritance errors) are represented in the STATUS info field. 
+
+3.) MIE Checks. If apparent violations of Mendelian inheritance are observed, first VarScan attempts to re-call the trio with relaxed settings to obtain compatible genotypes. If this fails, the FILTER field will be mendelError.
+
+Notes: 
+-The --min-coverage parameter is set to 12 and applies to ALL three samples (otherwise the site won't be called). This prevents a lot of power-of-detection issues at low coverage. For even more conservative results, set --min-coverage to 20.
+
+USE THE FILTER!
+Note, if you use VarScan you should also employ the false-positive filter described in the VarScan 2 publication.
+-For somatic mutations, filter with the Tumor BAM. For LOH and Germline, filter with the Normal BAM
+-For de novo mutations (trio calling), filter with the child BAM.
+See the fpfilter.pl and fpfilter-help.txt files here: https://sourceforge.net/projects/varscan/files/scripts/
+The filter requires the bam-readcount utility: https://github.com/genome/bam-readcount
+
+LICENSE
+VarScan 2 is licensed under the Non-Profit Open Software License 3.0 (NPOSL-3.0)
+
+CITING VARSCAN
+If you use VarScan, please note the version number and cite this publication along with the URL:
+
+Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 
+VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. 
+Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. 
+http://varscan.sourceforge.net
+
+
diff --git a/debian/rules b/debian/rules
index 6712aa4..33eb9f2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,5 +9,8 @@ override_dh_auto_build:
 	dh_auto_build
 	rm -f build.xml
 
+override_dh_installchangelogs:
+	dh_installchangelogs debian/release-notes.txt
+
 %:
 	dh $@ --with javahelper

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