processSomatic: processSomatic

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run VarScan2 (processSomatic)

Usage

processSomatic(fns.vcf, output.dir, min_tumor_freq=0.1, max_normal_freq=0.05, p_value=0.07, run.cmd=TRUE, mc.cores=1)

Arguments

fns.vcf	varscan output file path
output.dir	Output directory
min_tumor_freq	A parameter value for –min-tumor-freq in varscan2. Minimum variant allele frequency in tumor (default:0.10)
max_normal_freq	A parameter value for –max-normal-freq in varscan2. Maximum variant allele frequency in normal (default:0.05)
p_value	A parameter value for –p-value in varscan2. P-value for high-confidence calling (default:0.07)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

processSomatic will separate a somatic output file by somatic_status (Germline, Somatic, LOH). Somatic mutations will further be classified as high-confidence (.hc) or low-confidence (.lc).

References

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

See Also

{http://varscan.sourceforge.net/

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.