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VarScan.v2.3.9.jar (111.4 kB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| fpfilter-help.txt | 2012-03-06 | 1.7 kB | |
| mergeSegments-help.txt | 2012-03-06 | 2.3 kB | |
| mergeSegments.pl | 2012-03-06 | 14.2 kB | |
| fpfilter.pl | 2012-01-26 | 16.3 kB | |
| Totals: 4 Items | 34.5 kB | 0 | |
RELEASE NOTES FOR VARSCAN V2.3.1 09-August-2012 VarScan v2.3.1 includes several feature enhancements and bug fixes: -Expanded VCF compatibility for filter, somaticFilter, and processSomatic commands -Extended the optional VCF fields for mpileup2snp, mpileup2indel, and mpileup2cns output to include all VarScan fields -Made it possible to provide a list of sample names for VCF output for mpileup2* commands. -Expanded copyCaller functionality to filter by depth and output candidate homozygous deletions -Fixed a bug in the indel-filtering functionality of the filter command -Fixed European locale parsing errors in the copyCaller command Note, if you use VarScan you should also employ the false-positive filter described in the VarScan 2 publication. 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)