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VarScan is a command-line tool for identifying simple nucleotide polymorphisms (SNPs) and Indels in the human genome. VarScan makes many sequence alignment tools accessible via the command line. Among its features is a likelihood based algorithm that incorporates information about indels to account for the possibility that some small variants may be due to the deletion of a single nucleotide.
When scanning the human genome, VarScan includes multiple options for filtering, such as quality score, overlapping paired-end, allele frequency, and probe summarization. VarScan is a free tool.
(Java)
usage: java net.sf.varscan.VarScan [COMMAND] [OPTIONS]
The commands available can identify SNPs and Indels from a Sam Tools pileup file (pileup2snp and pileup2indel), along with SNPs and Indels from an mpileup file (mpileup2snp and mpileup2indel), as well as call consensus and variants from a pileup and mpileup file (pileup2cns and mpileup2cns).
Moreover, you can call germline or somatic variants from tumor-normal pileups (somatic), determine the relative tumor copy number from tumor-normal pileups (copynumber), get read counts for a list of variants from a pileup file (readcounts), filter SNPs by coverage, frequency, p-value and other criteria (filter), and filter somatic variants for clusters or Indels (somaticFilter).
Lastly, it’s possible to isolate germline, LOH or somatic calls from the output (processSomatic), call copy number changes from the somatic copy number output (copyCaller), compare two lists with positions or variants (compare), as well as restrict the pileup, SNPs or Indels to ROI positions (limit).
VarScan Description:

VarScan is a command-line tool for identifying simple nucleotide polymorphisms (SNPs) and Indels in the human genome. VarScan makes many sequence alignment tools accessible via the command line. Among its features is a likelihood based algorithm that incorporates information about indels to account for the possibility that some small variants may be due to the deletion of a single nucle

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