Clinvar Mapping
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?
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Pierre Lindenbaum
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Shweta •
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Shweta •
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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
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