VarScan is an open source tool for variant detection that is compatible with several short read aligners. It is capable of detecting SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples. VarScan2 detects somatic mutations and copy number alterations (CNAs) in exome data from tumor–normal pairs.

References:

• Daniel C. Koboldt, Ken Chen, Todd Wylie, David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson and Li Ding
  VarScan: variant detection in massively parallel sequencing of individual and pooled samples
  Bioinformatics, 2009, 25(17), pp.2283-2285.
• Daniel C. Koboldt, Qunyuan Zhang, David E. Larson, Dong Shen, Michael D. McLellan, Ling Lin, Christopher A. Miller, Elaine R. Mardis, Li Ding, and Richard K. Wilson
  VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
  Genome Res. 2012, 22, pp.568-576.

• VarScan Github page

• Module Name: VarScan (see the modules page for more information)
• Unusual environment variables set
  • VARSCAN_BIN       VarScan executable directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3316 ~]$ module load VarScan

[user@cn3316 ~]$ URL="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq"
[user@cn3316 ~]$ wget $URL/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam -O myData1.bam
[user@cn3316 ~]$ wget $URL/wgEncodeUwRepliSeqBg02esG2AlnRep1.bam -O myData2.bam
[user@cn3316 ~]$ samtools sort  myData1.bam > myData1_sorted.bam 
[user@cn3316 ~]$ samtools sort  myData2.bam > myData2_sorted.bam 
[user@cn3316 ~]$ ln -s /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa hg19.fa
[user@cn3316 ~]$ samtools mpileup -B -f hg19.fa  myData1_sorted.bam  > myData1.pileup
[user@cn3316 ~]$ samtools mpileup -B -f hg19.fa  myData2_sorted.bam  > myData2.pileup

[user@cn3316 ~]$varscan somatic myData1.pileup myData2.pileup --output-snp snp --output-indel indel
Normal Pileup: myData1.pileup
Tumor Pileup: myData2.pileup
NOTICE: While dual input files are still supported, using a single mpileup file (normal-tumor) with the --mpileup 1 setting is strongly recommended.
Min coverage:   8x for Normal, 6x for Tumor
Min reads2:     2
Min strands2:   1
Min var freq:   0.2
Min freq for hom:       0.75
Normal purity:  1.0
Tumor purity:   1.0
Min avg qual:   15
P-value thresh: 0.99
Somatic p-value:        0.05
52831015 positions in tumor
52831015 positions shared in normal
225836 had sufficient coverage for comparison
0 were called Reference
0 were mixed SNP-indel calls and filtered
225836 were called Germline
0 were called LOH
0 were called Somatic
0 were called Unknown
0 were called Variant
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. VarScan.sh). For example:

#!/bin/bash
module load VarScan
varscan somatic myData1.pileup myData2.pileup --output-snp snp12 --output-indel indel12
varscan somatic myData3.pileup myData4.pileup --output-snp snp34 --output-indel indel34
...

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] VarScan.sh