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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Appropriate WGS Mutect normal_panel
I'm running mutect1 with WGS and am trying to figure out what the appropriate attribute to use for the normal_panel is. I'm guessing it might be this 1000 genomes file ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/, but am not sure. Any advice would be appreciated! Most of the information out there seems geared towards exomes.