bt.tag: Annotates a BAM file based on overlaps with multiple...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in -i.

Description

Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in -i.

Usage

bt.tag(
  i,
  files,
  s = NULL,
  S = NULL,
  f = NULL,
  tag = NULL,
  names = NULL,
  scores = NULL,
  intervals = NULL,
  labels = NULL,
  output = NULL
)

Arguments

i	<BAM>
files	FILE1 .. FILEn
s	Require overlaps on the same strand. That is, only tag alignments that have the same strand as a feature in the annotation file(s).
S	Require overlaps on the opposite strand. That is, only tag alignments that have the opposite strand as a feature in the annotation file(s).
f	Minimum overlap required as a fraction of the alignment. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
tag	Dictate what the tag should be. Default is YB. - STRING (two characters, e.g., YK)
names	Use the name field from the annotation files to populate tags. By default, the -labels values are used.
scores	Use the score field from the annotation files to populate tags. By default, the -labels values are used.
intervals	Use the full interval (including name, score, and strand) to populate tags. Requires the -labels option to identify from which file the interval came.
labels	LAB1 .. LABn
output	Output filepath instead of returning output in R.

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