HaplotypeCaller Exome Region File

Data sources and code used to generate the exome region file used by GATK HaplotypeCaller in WES runs.

VEP v101

Accessed 2021-10-21.

VEP v101 archive website.

VEP v101 gtf file:

Homo_sapiens.GRCh38.101.gtf.gz

A copy of this file is also stored within the exome_regions folder of the cgap-annotations s3 bucket.

Reference File Creation

To transform this VEP gtf file into a comprehensive bed file of all possible transcripts and UTR regions, one python script and two BEDTools (v2.30.0) commands were used.

bgzip -d Homo_sapiens.GRCh38.101.gtf.gz
python exome_hg38_region_of_interest.py Homo_sapiens.GRCh38.101.gtf regions_bed_final.bed
bedtools sort -i regions_bed_final.bed > sort_regions_bed_final.bed
bedtools merge -i sort_regions_bed_final.bed > merge_sort_regions_bed_final.bed

exome_hg38_region_of_interest.py is available in this repository in /genes/exome_regions/.