varscan: varscan

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

Description

A wrapper function to run VarScan2

Usage

varscan(fn.pileup, output.dir, sample.name, min_coverage_normal=8, min_coverage_tumor=6, min_var_freq=0.10, min_freq_for_hom=0.75, somatic_p_value=0.05, strand_filter=0, run.cmd=TRUE, mc.cores=1)

Arguments

fn.pileup	samtools mpileup output file path
output.dir	Output directory
sample.name	A character vector for the sample names
min_coverage_normal	A parameter value for –min-coverage-normal in VarScan2. Minimum coverage in normal to call somatic (default:8)
min_coverage_tumor	A parameter value for –min-coverage-tumor in VarScan2. Minimum coverage in tumor to call somatic (default:6)
min_var_freq	A parameter value for –min-var-freq in VarScan2. Minimum variant frequency to call a heterozygote (default:0.10)
min_freq_for_hom	A parameter value for –min-freq-for-hom in VarScan2. Minimum frequency to call homozygote (default:0.75)
somatic_p_value	A parameter value for –somatic-p-value in VarScan2. P-value threshold to call a somatic site (default:0.05)
strand_filter	A parameter value for –strand-fiter in VarScan2. If set to 1, removes variants with > 90 percent strand bias(default:0)
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

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome sequencing data.

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.