@genebe/ccrs_hg19:0.0.1

Constrained Coding Regions based on 123,136 human exomes from gnomAD

If you use CCRs in any way, please cite the paper:

Havrilla, J.M., Pedersen, B.S., Layer, R.M. & Quinlan, A.R. A map of constrained coding regions in the human genome. Nature Genetics (2018). doi:10.1038/s41588-018-0294-6

Instructions

Data downloaded from https://s3.us-east-2.amazonaws.com/ccrs/ccr.html

and then

zcat ccrs.autosomes.v2.20180420.bed.gz | head -n1 > ready.bed
zcat ccrs.autosomes.v2.20180420.bed.gz | tail -n +2 >> ready.bed
zcat ccrs.xchrom.v2.20180420.bed.gz | tail -n +2 >> ready.bed
cut -f1-4 ready.bed > ready-cut.bed

And import using:

java -jar GeneBeClient.jar annotation create-from-tsv --name ccrs_hg19 --owner @genebe --version 0.0.1 --columns "#chrom/chr:TEXT" ccr_pct/ccrs:FLOAT32 --genome GRCh37 --species homo_sapiens --input /wum/pio/annotatios/ccrs/2025/hg19/ready-cut.bed --database-type REGION