Question: How/Where to get the "known Variant VCF file" for base recalibration of Human Mitochondrial Genome with GATK 4
0
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1048 users visited in the last hour
_