variants: variants

In mskilab/skitools: Various mskilab R utilties

variants

Description

Call substitutions and indels from contigs

Calls substitutions from contigs by comparing DNAStringSet ref against reference sequence ref via RSeqLib::BWA

The caller is IUPAC "ambiguity code aware" meaning that for every instance of ambiguity in the query and reference it will output the cartesian product of all mismatching variants (iupac = TRUE) otherwise it will treat those bases literally.

Note: not recommended to use on reads, only for contigs, i.e. will not scale to millions of reads

Usage

variants(query, ref, expand.iupac = TRUE, verbose = FALSE)

Arguments

query	DNAStringSet of query
ref	DNASTringSet of ref
expand.iupac	logical flag (TRUE) specifying whether to expand iupac for computing SNV in query and reference

Value

GRanges in ref coordinates of SNV and indels

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.