Clinvar Mapping

Question

[Shweta]

I have a list of genes. I want to identify reported variants using the ClinVar database. Can anyone help me with how can i automate clinvar mapping to classify my gene list with their associated variants - [athogenic, likely pathogenic, and benign?

Answer 1

[Pierre Lindenbaum]

get a BED file for your bed.

get the indexed VCF for clinvar: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/

Query the VCF for clinvar using bcftools view --regions-file genes.bed clinvar.vcf.gz