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@dkoboldt dkoboldt released this 26 May 17:45
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2.4.2
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RELEASE NOTES FOR VARSCAN V2.4.2

26-May-2016

VarScan v2.4.2 is the current release
VarScan v2.4.1 is the previous release
VarScan v2.4.0 was the first release to VarScan's new home at GitHub, http://dkoboldt.github.io/varscan/
VarScan v2.3.9 and prior releases will persist on SourceForge, as will the support forums and other resources.

LICENSE
VarScan 2 is free for non-commercial use by academic, government, and non-profit/not-for-profit institutions.
A commercial version of the software is available, and licensed through the Office of Technology Management at
Washington University School of Medicine. For more information, please contact:

Paul Carter, Business Development Director
[email protected]
+1 314-362-5426
https://otm.wustl.edu/for-industry/tools/

VERSION 2.4.2 CHANGES
The primary changes are minor bugfixes for user-reported issues:

1.) Better handling of mal-formed mpileup lines in VarScan copynumber

2.) Addressing missing segregation STATUS codes in VarScan trio and the addition of a new code (0) for "Unknown")

3.) Addressing a VCF format issue for somatic mutation calling, in which multi-allelic sites (classified as "UNKNOWN") were reported
in non-standard VCF format (with forward slashes in the ALT column). VarScan 2 somatic should now report multiple variant alleles
using the ALT1,ALT2 format and the genotype fields for normal and tumor samples should reflect the appropriate variant allele.

REMINDER: PLEASE USE THE FALSE POSITIVE FILTER
The scientific basis of this filter is described in the VarScan 2 publication. It will improve
the precision of variant and mutation calling by removing artifacts associated with short-read alignment.
-For somatic mutations, generate bam-readcounts with the Tumor BAM. For LOH and Germline, generate readcounts with the Normal BAM
-For de novo mutations (trio calling), generate readcounts with the child BAM.
The filter requires the bam-readcount utility: https://github.com/genome/bam-readcount

USAGE: java -jar VarScan.jar fpfilter [variant file] [readcount file] OPTIONS
variant file - A file of SNPs or indels in VarScan-native or VCF format
readcount file - The output file from bam-readcount for those positions
_For detailed filtering instructions, please visit http://varscan.sourceforge.net_

OPTIONS:
--output-file       Optional output file for filter-pass variants
--filtered-file     Optional output file for filter-fail variants
--dream3-settings   If set to 1, optimizes filter parameters based on TCGA-ICGC DREAM-3 SNV Challenge results
--keep-failures     If set to 1, includes failures in the output file

FILTERING PARAMETERS:
--min-var-count     Minimum number of variant-supporting reads [4]
--min-var-count-lc  Minimum number of variant-supporting reads when depth below somaticPdepth [2]
--min-var-freq      Minimum variant allele frequency [0.05]
--max-somatic-p     Maximum somatic p-value [0.05]
--max-somatic-p-depth   Depth required to test max somatic p-value [10]
--min-ref-readpos   Minimum average read position of ref-supporting reads [0.1]
--min-var-readpos   Minimum average read position of var-supporting reads [0.1]
--min-ref-dist3     Minimum average distance to effective 3' end (ref) [0.1]
--min-var-dist3     Minimum average distance to effective 3' end (var) [0.1]
--min-strandedness  Minimum fraction of variant reads from each strand [0.01]
--min-strand-reads  Minimum allele depth required to perform the strand tests [5]
--min-ref-basequal  Minimum average base quality for ref allele [15]
--min-var-basequal  Minimum average base quality for var allele [15]
--min-ref-avgrl     Minimum average trimmed read length for ref allele [90]
--min-var-avgrl     Minimum average trimmed read length for var allele [90]
--max-rl-diff       Maximum average relative read length difference (ref - var) [0.25]
--max-ref-mmqs      Maximum mismatch quality sum of reference-supporting reads [100]
--max-var-mmqs      Maximum mismatch quality sum of variant-supporting reads [100]
--max-mmqs-diff     Maximum average mismatch quality sum (var - ref) [50]
--min-ref-mapqual   Minimum average mapping quality for ref allele [15]
--min-var-mapqual   Minimum average mapping quality for var allele [15]
--max-mapqual-diff  Maximum average mapping quality (ref - var) [50]

DREAM-3 SETTINGS FOR FPFILTER
Please note the --dream3-settings parameter for fpfilter, which (if set to 1) will optimize the
false positive filter settings based on the fine-tuning we did for the TCGA-ICGC DREAM-3
SNV Challenge. See the "in silico 3" dataset described here:
https://www.synapse.org/#!Synapse:syn312572/wiki/62018
This dataset modeled 100% tumor purity, but three subclones at 50%, 33%, and 20% variant allele frequency.
Optimal VarScan settings were established as follows:
For SAMtools:
mpileup -B (disables BAQ)

For VarScan somatic:
    --min-coverage 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --strand-filter 0

For VarScan fpfilter:
    --min-var-count = 3
    --min-var-count-lc = 1
    --min-strandedness = 0
    --min-var-basequal = 30
    --min-ref-readpos = 0.20
    --min-ref-dist3 = 0.20
    --min-var-readpos = 0.15
    --min-var-dist3 = 0.15
    --max-rl-diff = 0.05
    --max-mapqual-diff = 10
    --min-ref-mapqual = 20
    --min-var-mapqual = 30
    --max-var-mmqs = 100
    --max-ref-mmqs = 50

CITING VARSCAN
If you use VarScan, please note the version number and cite this publication along with the
version-appropriate 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.

https://github.com/dkoboldt/varscan (v2.4.0 and beyond)
or
http://varscan.sourceforge.net (v2.3.9 and before)

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