collapsePairs {CrispRVariants} | R Documentation

## Internal CrispRVariants function for collapsing pairs with concordant indels

### Description

Given a set of alignments to a target region, finds read pairs. Compares insertion/deletion locations within pairs using the cigar string. Pairs with non-identical indels are excluded. Pairs with identical indels are collapsed to a single read, taking the consensus sequence of the pairs.

### Usage

    collapsePairs(alns, use.consensus = TRUE, keep.unpaired = TRUE,
      verbose = TRUE, ...)

### Arguments

`alns` | A GAlignments object. We do not use GAlignmentPairs because amplicon-seq can result in pairs in non-standard pairing orientation. Must include BAM flag, must not include unmapped reads.
`use.consensus` | Should the consensus sequence be used if pairs have a mismatch? Setting this to be TRUE makes this function much slower (Default: TRUE)
`keep.unpaired` | Should unpaired and chimeric reads be included? (Default: TRUE)
`verbose` | Report statistics on reads kept and excluded
`...` | Additional items with the same length as alns, that should be filtered to match alns.

### Value

The alignments, with non-concordant pairs removed and concordant pairs represented by a single read.

### Author(s)

Helen Lindsay

[Package CrispRVariants version 1.20.0 Index]