bt.bamtobed: Converts BAM alignments to BED6 or BEDPE format.

View source: R/bt.bamtobed.R

bt.bamtobedR Documentation

Converts BAM alignments to BED6 or BEDPE format.

Description

Converts BAM alignments to BED6 or BEDPE format.

Usage

bt.bamtobed(
  i,
  bedpe = NULL,
  mate1 = NULL,
  bed12 = NULL,
  split = NULL,
  splitD = NULL,
  ed = NULL,
  tag = NULL,
  color = NULL,
  cigar = NULL,
  output = NULL
)

Arguments

i

<bam>

bedpe

Write BEDPE format. - Requires BAM to be grouped or sorted by query.

mate1

When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE "block".

bed12

Write "blocked" BED format (aka "BED12"). Forces -split. http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1

split

Report "split" BAM alignments as separate BED entries. Splits only on N CIGAR operations.

splitD

Split alignments based on N and D CIGAR operators. Forces -split.

ed

Use BAM edit distance (NM tag) for BED score. - Default for BED is to use mapping quality. - Default for BEDPE is to use the minimum of the two mapping qualities for the pair. - When -ed is used with -bedpe, the total edit distance from the two mates is reported.

tag

Use other NUMERIC BAM alignment tag for BED score. - Default for BED is to use mapping quality. Disallowed with BEDPE output.

color

An R,G,B string for the color used with BED12 format. Default is (255,0,0).

cigar

Add the CIGAR string to the BED entry as a 7th column.

output

Output filepath instead of returning output in R.


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