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commit 2463a5b2a106a9e82e1ddaa3d312fc8b09e82062 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varscan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
