How to make exome frequency database like ExAC ?

Question

[kdjteda]

Hi, I have 300 exome-sequencing samples. I want to make a local frequency database for variants. How should i do ? I think maybe i should call all 500 samples jointly, but i would need a super computer to apply which i dont own . So, can i call the 500 samples seperately then merge the vcf into a big vcf file,then compute the alle frequency ? and how should i merge the vcf ? get the union or intersection ?

Answer 1

[Pierre Lindenbaum]

Use GATK to call 500 Gvcf : https://www.broadinstitute.org/gatk/guide/article?id=3893

[kdjteda]

thanks a lot for your answer, I will check the link .