mergeChimeras {CrispRVariants} | R Documentation

## mergeChimeras

### 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

[Package CrispRVariants version 1.14.0 Index]