README
Display ClinVar variants in HiGlass
Note: This is the source code for the ClinVar track only! You might want to check out the following repositories as well:
- HiGlass viewer: https://github.com/higlass/higlass
- HiGlass server: https://github.com/higlass/higlass-server
- HiGlass docker: https://github.com/higlass/higlass-docker
Installation
npm install higlass-clinvar
Data preparation
In order to bring a ClinVar vcf file (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/) into the required BED format, the following script can be used (make sure to adjust the file names in the script). A chrom sizes file is required.
python /scripts/extract_clinvar_data.py
The resulting bed file can be aggregated and ingested into a HiGlass server in the usual way:
clodius aggregate bedfile --chromsizes-filename hg38.txt --delimiter