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How to make exome frequency database like ExAC ?

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 ?

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updated by Pierre Lindenbaum Pierre Lindenbaum • written by kdjteda • kdjteda

1 answer

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by kdjteda • kdjteda

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