gatk_mutect2: Mapping to the Mutect2
In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description Usage Arguments Details See Also

Mapping to the Genome Analysis ToolKit (GATK) Mutect2 somatic mutation caller.

gatk_Mutect2(
  bam,
  reference,
  vcf,
  normal = NULL,
  pon = NULL,
  germline = NULL,
  ps = NULL,
  remake = FALSE
)

`bam`	one or more sam/bam files to where mutations are to be called and optionally matched normal samples when `Mutect2` is called in the "Tumor with Matched Normal" mode
`reference`	a reference fasta (`.fas`) file to which the sam/bam file was mapped
`vcf`	an output `vcf` file with called mutations
`normal`	optional sample names (`RG` sam/bam tag) of the matched normal samples
`pon`	optional the 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.
`remake`	optional remake the output if it already exists

Somatic mutations include short nucleid variations (SNV) and insertion-deletions (inserts).

GATK a GATK binding GATKR6 a GATK binding in the form of R6 class gatk_snv a convenience function simplifying SNV calling with gatk_Mutect2 gatk_prepare and gatk_make_pon for other convenience functions utilizing the GATK calls

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