mergeChimeras: mergeChimeras

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

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

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

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.