Question: How to make exome frequency database like ExAC ?
0
gravatar for kdjteda
3.6 years ago by
kdjteda0
kdjteda0 wrote:

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 ?

genome • 1.3k views
ADD COMMENTlink modified 3.6 years ago by Pierre Lindenbaum125k • written 3.6 years ago by kdjteda0
1
gravatar for Pierre Lindenbaum
3.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

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

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ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum125k

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

ADD REPLYlink written 3.6 years ago by kdjteda0
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