Is it possible to use vcf file as the input of the GenomeSTRiP?

Dear GenomeSTRiP users,

I am using Genome STRiP for the cohorts that I only have the bcf or vcf files. Is there anyway to use the vcf files as the input to Genome STRiP? Because I rarely saw people can convert vcf back to bam files... Thank you very much.

Best regards,
Wusheng

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    Can you explain more what you want to do?

    You can use a VCF as input to Genome STRiP genotyping. It has to conform to the format Genome STRiP expects. If conversion is needed, it is usually easy. But genotyping requires the bam/cram files (or if you want to do read-depth-only genotyping, you can do this using just the preprocessing output without needed access to the bam/cram files).

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