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.
can VariantsToTable output the raw genotype call (i.e., 0/1) rather than the actual basecall (A/T)?
I'm interested in getting simple "heterozygous" or "homozygous" designations for all of the samples/SNPs in my multisample VCF file. In the past, I have been using the -GF GT option in VariantsToTable, and then annotating my basecalls in Excel as either heterozygous or homozygous. This takes forever since Excel isn't really built for big data like this. Is there a simple way to output all of the SNPs as 0/1, 0/0, 0/1, or 1/1 instead of C/A, A/A, G/T, C/C?