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