Regarding ClinVar's VCF file

Question

[singhankit973]

I was having a look at the ClinVar VCF file with the intent to make a disease-gene association matrix. For that purpose, I wanted to focus only on pathogenic/likely pathogenic variants. But the problem I am facing is that in case of conflicting associations in the CLNSIGCONF field, the values of the field are not listed in the same order as the order of the diseases in CLNDN field. I wanted to ask if there is any way I can get 1:1 association between the two such that I get to know if the variant is benign with respect to a disease and likely benign or pathogenic with respect to another?

[Jeremy Leipzig]

the vcf is kind of an artificially assembled convenience file. have you looked at the variant_summary here: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/