Annotates a BED file with HGVS-like coordinates
usage: bed2hgvs.R [-h] -b BEDFILE [-o OUTNAME] [-O OUTDIR] [-p PREFERRED_TX]
Annotates bedfiles with ranges in HGVS-like format
arguments:
-h, --help show this help message and exit
-b BEDFILE, --bedfile BEDFILE
path to BED file (REQUIRED)
-o OUTNAME, --outname OUTNAME
output file name
-O OUTDIR, --outdir OUTDIR
output file directory
-p PREFERRED_TX, --preferred_tx PREFERRED_TX
path to tsv file of preferred transcripts <GENENAME>
<REFSEQID>. One REFSEQID per row
Returns a TSV file of bed intervals with HGVS-like annotations on the 4th column. If a file of preferred transcripts (RefSeq) are given, any conflict between given transcripts and those stored in the internal RefSeq database will be written to file:
.rbed2hgvs.missing
Given RefSeq transcipts - irrespective of version - was not found in the DB
.rbed2hgvs.version
Transcripts were found, but versions were conflicting
This script requires R package Rbed2HGVS (https://github.com/cwmedway/Rbed2HGVS). Once the shared conda environment (/env/bed2hgvs.yml) is active, Rbed2HGVS can be installed:
devtools::install_github(repo = "cwmedway/Rbed2HGVS", dependencies = T)