Conver ClinVar VCF to tsv file and save to database. transform_vcf_to_tsv.py is a generic script to transform vcf to tsv, could be used on other files.
To download and generate clinvar files, run make clinvar/input/clinvar_grch37_input.vcf.gz to download vcf files first, then run make clinvar/export/clinvar_grch38.tst.gz.
When generating clinvar files, there might be some warnings: [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.), I guess it's ok to ignore them for now because everything works as expected. Solutions to fix(haven't verified yet): https://www.biostars.org/p/407384/
Fix: https://github.com/knowledgesystems/signal/issues/104
Conver ClinVar VCF to tsv file and save to database.
transform_vcf_to_tsv.pyis a generic script to transform vcf to tsv, could be used on other files.To download and generate clinvar files, run
make clinvar/input/clinvar_grch37_input.vcf.gzto download vcf files first, then runmake clinvar/export/clinvar_grch38.tst.gz.When generating clinvar files, there might be some warnings:
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.), I guess it's ok to ignore them for now because everything works as expected. Solutions to fix(haven't verified yet): https://www.biostars.org/p/407384/Reference: https://github.com/sigven/vcf2tsv https://github.com/brentp/cyvcf2