Entering edit mode
4.5 years ago
lakshika125
•
0
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
Looks like Broad provides them via a google cloud bucket. I am linking an upstream post follow the links to
resource bundle
.