bt.multicov: Counts sequence coverage for multiple bams at specific loci.

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Counts sequence coverage for multiple bams at specific loci.

Description

Counts sequence coverage for multiple bams at specific loci.

Usage

bt.multicov(
  bams,
  bed,
  split = NULL,
  s = NULL,
  S = NULL,
  f = NULL,
  r = NULL,
  q = NULL,
  D = NULL,
  F = NULL,
  p = NULL,
  output = NULL
)

Arguments

bams	aln.1.bam aln.2.bam ... aln.n.bam
bed	<bed/gff/vcf>
split	Treat "split" BAM or BED12 entries as distinct BED intervals.
s	Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand.
S	Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand.
f	Minimum overlap required as a fraction of each -bed record. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
r	Require that the fraction overlap be reciprocal for each -bed and B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90 percent of each -bed and the -bed record _also_ overlaps 90 percent of B.
q	Minimum mapping quality allowed. Default is 0.
D	Include duplicate reads. Default counts non-duplicates only
F	Include failed-QC reads. Default counts pass-QC reads only
p	Only count proper pairs. Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.