varbase: Returns variant bases and ranges from GRanges or...

In mskilab/bamUtils: Utility functions for manipulating BAMs

Returns variant bases and ranges from GRanges or GappedAlignments input

Description

Takes GRanges or GappedAlignments object "reads" and uses cigar, MD, seq fields to return variant bases and ranges

Returns GRangesList (of same length as input) of variant base positions with character vector $varbase field populated with variant bases for each GRanges item in grl[[k]], with the following handling for insertions, deletions, and substitution GRange's:

Substitutions: nchar(gr$varbase) = width(gr) of the corresponding var Insertions: nchar(gr$varbase)>=1, width(gr) ==0 Deletions: gr$varbase = ”, width(gr)>=1

Each GRanges also has $type flag which shows the cigar string code for the event i.e. S = soft clip –> varbase represents clipped bases I = insertion –> varbase represents inserted bases D = deletion –> varbase is empty X = mismatch –> varbase represents mismatched bases

Usage

varbase(reads, soft = TRUE, verbose = TRUE)

Arguments

reads	GenomicRanges or GRangesList or GappedAlignments or data.frame/data.table reads to extract variants from
soft	boolean Flag to include soft-clipped matches (default = TRUE)
verbose	boolean verbose flag (default = TRUE)

mskilab/bamUtils documentation built on Sept. 28, 2022, 3:45 p.m.