bamreadcounts: extract nucleotide counts for targeted variants from the BAM...

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

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.

PoisonAlien/maftools documentation built on Nov. 5, 2024, 4:12 p.m.