Download Latest Version VarScan.v2.3.9.jar (111.4 kB)
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Name Modified Size InfoDownloads / Week
scripts 2012-03-06
6 6 weekly downloads
VarScan.v2.4.0.description.txt 2015-08-20 4.5 kB
2 2 weekly downloads
VarScan.v2.3.9.jar 2015-06-03 111.4 kB
16 16 weekly downloads
VarScan.v2.3.9.description.txt 2015-06-03 3.6 kB
2 2 weekly downloads
VarScan.v2.3.9.source.jar 2015-06-03 199.1 kB
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VarScan.v2.3.8.jar 2015-04-29 111.4 kB
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VarScan.v2.3.8.source.jar 2015-04-29 199.1 kB
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VarScan.v2.3.8.description.txt 2015-04-29 3.2 kB
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VarScan.v2.3.7.jar 2014-07-15 102.6 kB
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VarScan.v2.3.7.source.jar 2014-07-15 183.4 kB
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VarScan.v2.3.7.description.txt 2014-07-15 1.8 kB
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VarScan.v2.3.6.jar 2013-07-29 102.4 kB
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VarScan.v2.3.6.source.jar 2013-07-29 183.0 kB
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VarScan.v2.3.6.description.txt 2013-07-29 3.6 kB
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VarScan.v2.3.5.jar 2013-03-20 89.1 kB
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VarScan.v2.3.5.source.jar 2013-03-20 159.0 kB
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VarScan.v2.3.5.description.txt 2013-03-20 1.5 kB
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VarScan.v2.3.4.jar 2013-01-30 88.4 kB
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VarScan.v2.3.4.source.jar 2013-01-30 157.3 kB
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VarScan.v2.3.4.description.txt 2013-01-30 866 Bytes
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VarScan.v2.3.3.jar 2012-11-08 88.2 kB
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VarScan.v2.3.3.description.txt 2012-11-08 849 Bytes
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VarScan.v2.3.3.source.jar 2012-11-08 156.9 kB
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VarScan.v2.3.2.description.txt 2012-08-31 578 Bytes
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VarScan.v2.3.2.jar 2012-08-31 87.7 kB
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VarScan.v2.3.2.source.jar 2012-08-31 156.1 kB
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VarScan.v2.3.1.readme.txt 2012-08-09 1.0 kB
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VarScan.v2.3.1.jar 2012-08-09 87.2 kB
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VarScan.v2.3.1.source.jar 2012-08-09 155.2 kB
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VarScan.v2.2.11.jar 2012-05-01 82.5 kB
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VarScan.v2.2.11.source.jar 2012-05-01 146.9 kB
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VarScan.v2.2.10.jar 2012-03-23 81.6 kB
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VarScan.v2.2.10.source.jar 2012-03-23 145.3 kB
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VarScan.v2.2.8.jar 2011-10-31 79.0 kB
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VarScan.v2.2.8.source.jar 2011-10-31 140.8 kB
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VarScan.v2.2.7.jar 2011-08-16 71.4 kB
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VarScan.v2.2.7.source.jar 2011-08-16 128.6 kB
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VarScan.v2.2.6.jar 2011-08-16 63.0 kB
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VarScan.v2.2.5.jar 2011-04-28 61.9 kB
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VarScan.v2.2.3.jar 2010-11-08 55.2 kB
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VarScan.v2.2.2.jar 2010-10-05 84.4 kB
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VarScan.v2.2.source.tar 2010-07-19 256.0 kB
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VarScan.v2.2.source.jar 2010-07-19 84.6 kB
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VarScan-Documentation.v2.2.tar 2010-04-27 174.1 kB
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VarScan.v2.2.jar 2010-04-27 44.9 kB
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VarScan-Documentation.v2.1.tar 2010-01-22 143.4 kB
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Totals: 46 Items   4.3 MB 26 
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)
Source: VarScan.v2.3.1.readme.txt, updated 2012-08-09