ClinVar data

How to update/download ClinVar data

VCF and index files

• Navigate to ClinVar downloads for GRCh37

• Then, make your current directory the genotoscope_data/ClinVar: cd /path2genotoscope_data/genotoscope_data/ClinVar

• There create a subfolder, with a descriptive name for the current version, for example clinvar_mar_2021: mkdir clinvar_mar_2021

• Download the compressed vcf and the index files:

  wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20211120.vcf.gz

  wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20211120.vcf.gz.tbi

Review status file

If review status stars system is updated:

• Navigate to the ClinVar review status description page
• Copy and paste the table 1 of the previous page to a .tsv file, to resemble the format of genotoscope_data/ClinVar/clinvar_review_stars.tsv
• Replace the current file, genotoscope_data/ClinVar/clinvar_review_stars.tsv, with the new one