https://daynefiler.com/categories/vcf/ Recent content in vcf on Dayne Filer, MD, PhD | Research Software & Scientific Computing Hugo -- gohugo.io en-US Mon, 30 Jul 2018 13:09:45 -0400 https://daynefiler.com/blog/gindexing/ Mon, 30 Jul 2018 13:09:45 -0400 https://daynefiler.com/blog/gindexing/ The gnomAD VCF files give information about the observed genotype counts, eg “GC_EAS” gives the genotype counts for individuals of East Asian decent as a comma-separated string. The order of the counts is determined by genotype-indexing. The above link gives an excellent discussion of getting the genotype index for the general case, regardless of ploidy number. Below is a brief discussion of haploid and diploid indices. Genotype-indexing works by first indexing the reference and alternative alleles, starting with the reference allele at 0.