bamreadcounts: extract nucleotide counts for targeted variants from the BAM...
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

bamreadcounts

R Documentation

extract nucleotide counts for targeted variants from the BAM file.

Description

Given a BAM file and target loci, 'bamreadcounts' fetches redcounts for A, T, G, C, Ins, and Del. Function name is an homage to https://github.com/genome/bam-readcount

Usage

bamreadcounts(
  bam = NULL,
  loci = NULL,
  zerobased = FALSE,
  mapq = 10,
  sam_flag = 1024,
  op = NULL,
  fa = NULL,
  nthreads = 4
)

Arguments

`bam`	Input bam file(s). Required.
`loci`	Loci file. Can be a tsv file or a data.frame. First two columns should contain chromosome and position (by default assumes coordinates are 1-based)
`zerobased`	are coordinates zero-based. Default FALSE.
`mapq`	Map quality. Default 10
`sam_flag`	SAM FLAG to filter reads. Default 1024
`op`	Output file basename. Default parses from BAM file
`fa`	Indexed fasta file. If provided, extracts and adds reference base to the output tsv.
`nthreads`	Number of threads to use. Each BAM file will be launched on a separate thread. Works only on Unix and macOS.