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pVCF versus gVCF

Hi. I want to calculate variant allele frequency in regulatory regions in colon cancer versus genomad data.

I googled too much and likely

gVCF is individual-level vcf

pVCF is population-level vcf

but this is too confusion

Can I use pVCF files for my project or I must use WGS/WES gVCF files?

vcf
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written by zizigolu zizigolu

1 answer

In the gatk ecosystem gvcfs are used to generate a pvcf. Search the gatk doc for genotypegvcf.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. Can I calculate variant allele frequency in a list of genomic coordinates using pVCF?

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written by zizigolu zizigolu

if you use gatk, the AF field should be present in the INFO field.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. As likely pVCF is population level files, you think is that possible to calculate VAF for certain patients IDs let's say belong to colon cancer only

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written by zizigolu zizigolu

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