bam2stat: Get basic BAM file statistics

In daewoooo/primatR: What the Package Does (TODO)

Get basic BAM file statistics

Description

This function takes as an input aligned reads in BAM and exports some useful statistics like depth of coverage and percentage of genome being coverged by reads.

Usage

bam2stat(
  bamfile,
  bamindex = paste0(bamfile, ".bai"),
  chromosomes = NULL,
  chunkSize = NULL,
  min.mapq = 10,
  filt.flag = 3328,
  filt.alt = FALSE
)

Arguments

bamfile	Bamfile with aligned reads.
bamindex	Bam-index file with or without the .bai ending. If this file does not exist it will be created and a warning is issued.
chromosomes	If only a subset of the chromosomes should be binned, specify them here.
chunkSize	Set for big BAMs to process them in smaller chunks.
min.mapq	Minimum mapping quality when importing from BAM files.
filt.flag	Filter out reads with a given flag.
filt.alt	Set to TRUE if you want to filter out alternative alignments defined in 'XA' tag.

Value

data.frame

Author(s)

David Porubsky

daewoooo/primatR documentation built on March 28, 2024, 6:41 a.m.