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Convert BED intervals between genome builds

Source: R/lift_bed.R
lift_bed.Rd

Use this utility to convert BED intervals between genome coordinate systems using liftOver. Only the chr/start/end fields of the input BED are used (strand is ignored). The output GRanges will have no associated seqinfo.

Usage

lift_bed(bed, chain, outfile = NULL)

Arguments

bed

Pathname of a BED file, or a GRanges (typically loaded from a BED file with rtracklayer::import.bed()).

chain

A UCSC-style chain file, or a Chain object (such as from rtracklayer::import.chain()).

outfile

If not NULL, the returned GRanges will be saved to the specified path using rtracklayer::export.chain().

Value

GRanges representing lifted intervals from input bed.

Details

A warning is given if the lifted intervals are less than 95% of the size of the original intervals. When the BED input represents sequencing target intervals, most of the input intervals will usually lift successfully.