bedtoolsr: Bedtools Wrapper

bt.pairtobed

R Documentation

Report overlaps between a BEDPE file and a BED/GFF/VCF file.

Description

Report overlaps between a BEDPE file and a BED/GFF/VCF file.

Usage

bt.pairtobed(
  a,
  b,
  abam = NULL,
  ubam = NULL,
  bedpe = NULL,
  ed = NULL,
  f = NULL,
  s = NULL,
  S = NULL,
  type = NULL,
  output = NULL
)

Arguments

`a`	<bedpe>
`b`	<bed/gff/vcf>
`abam`	The A input file is in BAM format. Output will be BAM as well. Replaces -a. - Requires BAM to be grouped or sorted by query.
`ubam`	Write uncompressed BAM output. Default writes compressed BAM. is to write output in BAM when using -abam.
`bedpe`	When using BAM input (-abam), write output as BEDPE. The default is to write output in BAM when using -abam.
`ed`	Use BAM total edit distance (NM tag) for BEDPE score. - Default for BEDPE is to use the minimum of of the two mapping qualities for the pair. - When -ed is used the total edit distance from the two mates is reported as the score.
`f`	Minimum overlap required as fraction of A (e.g. 0.05). Default is 1E-9 (effectively 1bp).
`s`	Require same strandedness when finding overlaps. Default is to ignore stand. Not applicable with -type inspan or -type outspan.
`S`	Require different strandedness when finding overlaps. Default is to ignore stand. Not applicable with -type inspan or -type outspan.
`type`	Approach to reporting overlaps between BEDPE and BED. either Report overlaps if either end of A overlaps B. - Default. neither Report A if neither end of A overlaps B. both Report overlaps if both ends of A overlap B. xor Report overlaps if one and only one end of A overlaps B. notboth Report overlaps if neither end or one and only one end of A overlap B. That is, xor + neither. ispan Report overlaps between [end1, start2] of A and B. - Note: If chrom1 <> chrom2, entry is ignored. ospan Report overlaps between [start1, end2] of A and B. - Note: If chrom1 <> chrom2, entry is ignored. notispan Report A if ispan of A doesn't overlap B. - Note: If chrom1 <> chrom2, entry is ignored. notospan Report A if ospan of A doesn't overlap B. - Note: If chrom1 <> chrom2, entry is ignored.
`output`	Output filepath instead of returning output in R.