VarScan

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Application data

Biological application domain(s) SNP discovery
Maintained? Yes
Input format(s) SAM, BAM
Output format(s) TXT
Software features SNP calling
Programming language(s) Java

Summary: VarScan, an open source tool for variant detection that is compatible with several short read align-ers.

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency.

Links


References

  1. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.. 2009. Bioinformatics
  2. . '. '


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