GIAB VCFs (v4.2.1) provides 0/1, 1/0 (ALT-heterozygous) & 1/1 (ALT- homozygous) genotypes (in addition 1/2, 2/1, & 2/2 where there are more than one ALT alleles). GIAB also provides a BED file where any other position not in the VCF can be consider high confidence homozygous reference.
I have a list of SNP rs IDs for which I need to extract the homozygous reference genotype, say for NA12878. Is there a simple why to achieve this?
The primary purpose is to allow genotype concordance measurement with a microarray platform, measure recall and precision.