mafcount: Wrapper around varcount adapted to tumor and normal "paired"...

In mskilab/bamUtils: Utility functions for manipulating BAMs

Wrapper around varcount adapted to tumor and normal "paired" bams

Description

Returns base counts for reference and alternative allele for an input tumor (and normal bam) and import MAF as a GRanges specifying substitutions

maf is a single width GRanges describing variants and field 'ref' (or 'Reference_Allele'), 'alt' (or 'Tum_Seq_Allele1') specifying reference and alt allele. maf is assumed to have width 1 and strand is ignored.

Usage

mafcount(
  tum.bam,
  norm.bam = NULL,
  maf,
  chunk.size = 100,
  verbose = TRUE,
  mc.cores = 1,
  ...
)

Arguments

tum.bam	string path to tumor sample, input to Bamfile()
norm.bam	optional string path to normal sample, input to Bamfile() (optional) (default = NULL)
maf	GRanges of imported MAF (e.g. output of read.delim or dt2gr(fread(MAF)))
chunk.size	integer Number of variants to extract from bam file at each iteration (default = 100)
verbose	logical Flag whether to print verbose output (default = TRUE)
mc.cores	integer Number of cores in mclapply (default = 1)
...	additional pparams to pass to varcount

Value

GRanges of MAF annotated with fields $alt.count.t, $ref.count.t, $alt.count.n, $ref.count.n

Author(s)

Marcin Imielinski

mskilab/bamUtils documentation built on Sept. 28, 2022, 3:45 p.m.