Data contained in VCF files have been used to infer ploidy in organisms where ploidy is either unknown or where variation in ploidy is a research question. Only the variable positions are reported in a VCF file, so we do not have total information about a genome or any particular region. We should have all of the heterozygous sites in our VCF file and this can be used to infer ploidy. At a diploid heterozygous position we expect to observe each allele at a ratio of 1/2. For example, at a G/C polymorphism sequenced at 20X coverage we would expect to observe each all approximately 10 times. At a triploid heterozygous position we would expect to observe alleles at a ratio of 1/3. For example, at a G/G/C polymorphism sequenced at 20X coverage we would expect to observe G approximately 13 times (we can not distinguish the two copies) and the C about 7 times. For tetraplods we would expect ratios of 1/4. This means that we can use the ratios of alleles observed at heterozygous positions to infer ploidy level.
Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.
USDA Agricultural Research Service, Horticultural Crops Research Lab.