RELEASE NOTES FOR VARSCAN V2.4.0 20-Aug-2015 VarScan v2.4.0 is 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 paulcarter@wustl.edu +1 314-362-5426 VERSION 2.4.0 CHANGES The major change to v2.4.0 is the implementation of a SmartFileReader class, which addresses a known bug in Java runtime that could cause VarScan to hang if given an empty input file. Hat tip to Bina Technologies for contributing this code. Minor issues addressed in the current release include: 1.) A correction in the way normal_reads2 values are counted when the mutation allele is not observed. Prior to this fix, a non-reference base would be counted as a variant allele even if it didn't match the actual mutation allele called in the tumor. Now, only observations of the tumor variant allele will be counted and go into the FET. 2.) Improved parameter-handling logic for two flags (--validation and --strand-filter), which previously were sometimes considered "turned on" if the user provided them, even if the value provided was a zero. 3.) Catching the rare ArrayIndexOutOfBoundsException errors thrown in the copynumber and trio functions when VarScan encountered incomplete mpileup columns. 4.) Addressed a typo-bug for the tumor-purity parameter which only had an effect if the user provided percentage values (e.g. 15) rather than fractions (e.g. 0.15). 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 --keep-failures If set to 1, include failures in the output file --min-var-count Minimum number of variant-supporting reads [4] --min-var-freq Minimum variant allele frequency [0.05] --min-var-readpos Minimum average read position of var-supporting reads [0.10] --min-var-dist3 Minimum average relative distance to effective 3' end [0.10] --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 [30] --min-var-basequal Minimum average base quality for var allele [30] --max-rl-diff Maximum average relative read length difference (ref - var) [0.25] --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 [30] --min-var-mapqual Minimum average mapping quality for var allele [30] --max-mapqual-diff Maximum average mapping quality (ref - var) [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)