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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.
Get a summary of SNV calls from MuTect2
Following the best practice of calling variants using MuTect2 with GATK3, I have stumbled upon the step 5 where we can filter our file for INDELs or SNPs. But I had issues with the contigs not being of the same length, so I switched to version 4 of GATK to get past the issue and successfully generated a VCF file only made of INDELs.
My question now is that how can we summarize the different results as shown in the step 5 ?
like the following :
Thanks a lot for your help.