Test-drive the GATK tools and Best Practices pipelines on Terra
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MuTect2 beta --germline_resource for build b37
Hi - I'm looking to run MuTect2 beta using the --germline_resource option. However, I've consistently used the b37 genome build throughout my analaysis, while the suggested resource (gnomad) appears to only be available for the hg19 build. So I'm wondering whether I should
1. Go ahead and use the gnomad hg19 files, despite the fact that my whole analysis has used the b37 build?
2. Lift over my existing gnomad vcfs from hg19 to b37? (In this case, I'd need an hg19tob37 liftOver file - I can't find one anywhere).
3. Use another germline resource?
I wonder which option you would recommend? Many thanks for your time.