VarScan2 Call SNPs from BAM (version 2.4.2.a)

Alignment file(s):

Mapped reads in BAM or SAM format.

Fasta Source:

Reference Genome used during alignment (FASTA):

Region specific parameters:

Let sambamba target specific genomic locations.

Advanced parameters:

For more advanced VarScan and sambamba settings.

Output format:

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. http://dx.doi.org/10.1101/gr.129684.111 http://www.ncbi.nlm.nih.gov/pubmed/19542151

VarScan requires mpileup input files, generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing can be by-passed using this tool. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan.

Input formats

VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files must have a reference genome (dbkey) in Galaxy.

Contact

The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands)