Variant detection in massively parallel sequencing data
Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh.
Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.
- Calls SNPs and Indels from SAMtools pileup files
- Filters variants by coverage, read depth, variant frequency, and base quality
- Determines somatic status (Somatic, Germline, LOH) for Tumor-Normal pairs
- Compares, merges, and intersects two lists of variants
- Limits variant calls to a set of target positions or target regions
- Free for non-commercial use.
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What's New in version 2.3.1
- 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