Question: How/Where to get the "known Variant VCF file" for base recalibration of Human Mitochondrial Genome with GATK 4
gravatar for lakshika125
15 months ago by
lakshika1250 wrote:

Im analysing human mitochondrial NGS sequences for germline variants. Im using GATK4 and wondering how should I get the " known variant VCF" of human mitochondrial DNA ; is there a way to do it if I dont have that file?

Also curious what should be done about the realignment step as that function is deprecated in GATK4

ADD COMMENTlink modified 21 days ago by Biostar ♦♦ 20 • written 15 months ago by lakshika1250

Looks like Broad provides them via a google cloud bucket. I am linking an upstream post follow the links to resource bundle.

ADD REPLYlink written 15 months ago by GenoMax95k
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