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.