gatk.combinevariants: gatk.combinevariants

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

Description

A wrapper function to run GATK (CombineVariants)

Usage

gatk.combinevariants(ref.fa, normal.vcf, minN=2, filteredrecordsmergetype="KEEP_IF_ANY_UNFILTERED", output.dir, run.cmd=TRUE, mc.cores=1)

Arguments

ref.fa	Reference fasta file
normal.vcf	Normal sample vcfs list
minN	Parameter value for -minN in GATK CombineVariants. Minimum number of samples to call the variant (default=2)
filteredrecordsmergetype	A parameter value for –filteredrecordsmergetype in GATK CombineVariants. Determines how to handle records seen at the same site in the VCF
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

The MuTect2 pipeline employs a "Panel of Normal" to identify additional germline mutations. This method enables a higher level of confidence to be assigned to somatic variants that are called by the MuTect2 pipeline.

Value

pon(panel of normal) vcf file

References

Sensitive detection of somatic point mutations in 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.