extendSVwithSimpRep: Extend SV coordinates using simple repeat annotation

In jmonlong/sveval: SV evaluation

Extend SV coordinates using simple repeat annotation

Description

Equivalent SVs are sometimes recorded as quite different variants because placed at different locations of a short tandem repeat. For example, imagine a large 100 bp tandem repeat in the reference genome. An expansion of 50 bp might be represented as a 50 bp insertion at the beginning of the repeat in the callset but at the end of the repeat in the truth set. Because they are distant by 100 bp they might not match. Instead of increasing the distance threshold too much, this function provides a more flexible way of matching variants by first extending them with nearby simple repeat. In this example, because we know of this tandem repeat, both insertions will be extended to span the full annotated reference repeat, hence ensuring that they are matched and compared (e.g. by reciprocal size or sequence alignment distance) short tandem repeat.

Usage

extendSVwithSimpRep(svs.gr, simprep.gr, max.dist.sr.join = 5, max.sv.dist = 5)

Arguments

svs.gr	a GRanges object with SV information (e.g. read by readSVvcf)
simprep.gr	a GRanges object with simple repeat information.
max.dist.sr.join	maximum distance to join nearby simple repeats. Default is 5 (bp)
max.sv.dist	maximum distance between SV and simple repeat to apply the extension. Default is 5 (bp)

Value

an updated GRanges object for svs.gr (start/end extended by simprep.gr)

Author(s)

Jean Monlong

jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.