Soft Repository

From SAM Tools pileup and mpileup files, you can use this application to identify and call SNPs and Indels. You can then filter the variants based on coverage, frequency, p-value and other criteria.

VarScan is a Java-based command-line tool used for identifying SNPs and Indels, which are DNA sequence variants that occur in populations. It is used for detecting and filtering germline variants, comparing read counts between samples, and calculating somatic status. VarScan can also merge and intersect two lists of variants.