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 GATK's VariantsToTable tool, 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? My ideal output would be a txt file in a grid similar to how VariantsToTable outputs data: top row is each sample, while first column is the variant coordinates.
if you start from a valid vcf file, you can get your desired output simply with this command:

    grep -v ^## input.vcf | cut -f1,2,10- | sed 's/:\S*//g'

`grep` to remove all headers but column names, `cut` to select chromosome+position+samples' columns, and `sed` to remove everything but GT from genotype columns.