- Call SNPs from an mpileup file based on user-defined parameters: use the mpileup2snp function
VarScan mpileup2snp Yoursample.pileup --min-coverage 10 --min-base-qual 30 --output-vcf 1 > Yoursample.vcf
If the option --output-vcf If set to 1, outputs in VCF format
Other possible OPTIONS:
--min-coverage Minimum read depth at a position to make a call [8]
--min-reads2 Minimum supporting reads at a position to call variants [2]
--min-avg-qual Minimum base quality at a position to count a read [15]
--min-var-freq Minimum variant allele frequency threshold [0.01]
--min-freq-for-hom Minimum frequency to call homozygote [0.75]
--p-value Default p-value threshold for calling variants [99e-02]
--strand-filter Ignore variants with >90% support on one strand [1]
--output-vcf If set to 1, outputs in VCF format
--variants Report only variant (SNP/indel) positions (mpileup2cns only) [0]
- Additional example details to perform somatic mutation calling:
Run SAMtools mpileup on the BAM files for normal and tumor
samtools mpileup –B –q 1 –f reference.fasta normal.bam tumor.bam >normal-tumor.mpileup
Run VarScan in somatic mode, providing the mpileup file (normal-tumor.mpileup) and a basename for output files (output.basename):
VarScan somatic normal-tumor.mpileup output.basename –min-coverage 10 –min-var-freq 0.08 –somatic-p-value 0.05
Many options available for somatic mutations, including mutation calling parameters (see table 3) or output field names (table 4) at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659/
Example of additional options for VCF output: --output-vcf Generate VCF output Set to 1 if VCF output is desired, or leave unset for VarScan's native output format, which is more human readable.
More information: http://varscan.sourceforge.net/using-varscan.html