gatk_snv: Identify and filter SNVs

In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description

Identify and filter single nucleotide variations in an input bam file.

Usage

gatk_snv(
  bam,
  reference,
  vcf,
  normal = NULL,
  pon = NULL,
  germline = NULL,
  ps = NULL,
  outdir = NULL,
  remake = FALSE
)

Arguments

bam	a sam/bam file prepared for variant calling
reference	a reference fasta (.fas) file to which the sam/bam file was mapped
vcf	an output gzipped vcf file containing only SNVs
normal	optional matched normal samples, either sam/bam files or normal sample names. If sam or bam files are provided, the sample names are retrieved from the files using the gatk_GetSampleName.
pon	optional Panel of Normals, see gatk_make_pon
germline	optional a vcf file of germline population contaning allelic fractions
ps	optional a parameter string passed to GATK Mutect2 call
outdir	optional an output directory for intermediate files
remake	optional remake the output if it already exists

Details

This is a convenience function that chains individual GATK calls to identify and filter SNVs. Following steps are performed:

• Mutect2 – calls variant using the GATK Mutect2 variant caller

• FilterMutectalls – filter the raw output from Mutect2

• vcftools – a non GATK call to preserve only single nucleotide variants

See Also

GATK and GATKR6 for a binding to indiviual GATK functions, gatk_prepare and gatk_make_pon for other convenience functions build on GATK calls, vcftools_filter() for more information on the vcftools call used in this function

bioDS/phyloRNA documentation built on Feb. 21, 2022, 3:28 p.m.