rmskAnnotate: Annotate REF/ALT sequence with RepeatMasker

In jmonlong/sveval: SV evaluation

Annotate REF/ALT sequence with RepeatMasker

Description

Extracts REF/ALT sequence from a VCF, runs RepeatMasker to annotate transposable elements and simple repeats, and annotates the original variants.

Usage

rmskAnnotate(svs.gr, nb.cores = 1, species = "human", docker.image = NULL)

Arguments

svs.gr	SVs. A GRanges or the path to a VCF file.
nb.cores	the number of cores that RepeatMasker should use. Default:1.
species	the species to use in RepeatMasker. Default: human.
docker.image	docker image with RepeatMasker. Default is NULL.

Details

This is a simple annotation where only the main repeat class is retrieved for each variant (covering most of the sequence).

RepeatMasker must be installed.

Value

an updated GRanges with new columns 'rmsk.name', 'rmsk.classfam' and 'rmsk.cov'.

Author(s)

Jean Monlong

Examples

## Not run: 
svs.gr = readSVvcf('calls.vcf', keep.ins.seq=TRUE, keep.ref.seq=TRUE)
svs.gr = rmskAnnotate(svs.gr)

## End(Not run)

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