collapsePairs: Internal CrispRVariants function for collapsing pairs with...

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

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

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