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VarScan2 Call INDELs from a mpileup file (version 2.4.2.a)
Mapped reads in mpileup format.
For more advanced VarScan settings.

VarScan 2.4.2

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.

Input formats

Alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: "database: hg19" for a link to hg19, or "database: ?" if the link is missing.


Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment.