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

View source: R/bt.tag.R

bt.tagR Documentation

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.