mergeChimeras: mergeChimeras

Description Usage Arguments Value Author(s)

View source: R/mergeChimeras.R

Description

Merges chimeric alignments where the individual segments border an unmapped region (a long deletion). If bases of the read are mapped to both ends of the gap, the multimapped reads are only included in the leftmost genomic segment. If there are more than max_unmapped unmapped bases between the mapped bases, the read is not considered mergeable. Currently experimental and only tested with reads mapped by bwa mem.

Usage

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mergeChimeras(bam, chimera_idxs = NULL, verbose = TRUE,
  max_read_overlap = 10, max_unmapped = 4, name = NULL)

Arguments

bam

A GenomicAlignments::GAlignments object

chimera_idxs

Indices of chimeric reads within bam

verbose

Should information about the number of mergeable alignments be printed? (Default: TRUE)

max_read_overlap

Maximum number of bases in a mergeable read that are aligned to two genomic locations (Default: 10)

max_unmapped

Maximum number of bases in a mergeable read that are unmapped and located between two mapped segments (Default: 4)

name

Name of the sample, used when reporting verbose output.

Value

A list of the merged and unmerged chimeric alignments

Author(s)

Helen Lindsay


CrispRVariants documentation built on Nov. 8, 2020, 11:09 p.m.