This script will annotate a BED file with refSeq NM and exons positions
Requires bedtools to be installed
sh MobiBedAnnotator.sh -r /path/to/ROI.bed
Arguments:
-r, --roi-bed: Your ROI BED file to be annotated. Must contain 4 columns.
Options:
-m, --master-bed: Path to the provided master.bed file which contains annotations for all coding HGNC genes (05/2018). Default cwd.
-b, --bedtools-path: Path to bedtools executables. Mandatory if bedtools not in path, optional otherwise
-o, --output: Desired name for the annotated output bed