mutect2: mutect2

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

Description

A wrapper function to run GATK (MuTect2) Processed through the variant calling as tumor-normal pairs.

Usage

run.mutect2(output.dir, ref.fa, tumor.bam, normal.bam, pon.vcf, cosmic.vcf, ref.dbSNP, contamination_fraction_to_filter=0.02, run.cmd=TRUE, mc.cores=1)

Arguments

output.dir	Output directory
ref.fa	Reference fasta file
tumor.bam	Tumor sample bam files
normal.bam	Bam files form normal samples obtained from a function gatk.mutect.normal
pon.vcf	Panel of normal samples obtained from a function gatk.combinedvariant
cosmic.vcf	Known variant sites of cosmic database vcf file
ref.dbSNP	Known SNP sites reference vcf
contamination_fraction_to_filter	A parameter value for –contamination_fraction_to_filter in GATK MuTect2. Fraction of contamination to aggressively remove (default=0.02)
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 designed to produce somatic variant calls only, and includes some logic to skip variant sites that are very clearly germline based on the evidence present in the Normal sample compared to the Tumor sample.

Value

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.