gatk.mutect2.normal: gatk.mutect2.normal

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

Description

A wrapper function to run GATK (MuTect2)

Usage

gatk.mutect2(normal.bam, sample.name, ref.dbSNP, cosmic.vcf, output.dir, run.cmd=TRUE, mc.cores=1)

Arguments

normal.bam	BAM files of normal samples
sample.name	A character vector for the sample names
ref.dbSNP	Known SNP sites reference vcf
cosmic.vcf	Known variant sites of cosmic database vcf file
output.dir	Output directory
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

MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller. This function takes normal samples as input to make the panel of normal (pon).

Value

Only normal sample vcf files.

References

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

See Also

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php

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