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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Which vcf file should be used? #58

Closed h170607 closed 1 year ago

h170607 commented 1 year ago

Hi, I read the web https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/, and am not sure which vcf file should be used. Can the vcf parameter use other databases? Can tbi files be generated with tools like tabix or bcftools etc?

dariober commented 1 year ago

Hi- As noted in the README, common_all.vcf.gz is generally a good choice. And yes you can use any vcf file with SNPs you think are more appropriate to your use case. Google vcf + tbi to find how to index them. Assuming your file is already sorted but not compressed, something like this should do:

bgzip in.vcf
tabix -p in.vcf.gz