pVCF versus gVCF

Question

[zizigolu]

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?

[LauferVA]

you might start by reading this: https://pubmed.ncbi.nlm.nih.gov/38057664/

Answer 1

[Pierre Lindenbaum]

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

[zizigolu]

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

[Pierre Lindenbaum]

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

[zizigolu]

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