This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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?