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

In PhanstielLab/bedtoolsr: Bedtools Wrapper

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.