How/Where to get the "known Variant VCF file" for base recalibration of Human Mitochondrial Genome with GATK 4
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4.5 years ago

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

Base recalibration known variant file • 1.5k views
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Looks like Broad provides them via a google cloud bucket. I am linking an upstream post follow the links to resource bundle.

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