Quantification of parent DNA contaminated by the other parent. (A) GroupE single nucleotide polymorphisms (SNPs) are defined as homo-alt genotypes in the offspring and variant allele frequency (VAF) <1 in the contaminated parent and homo-alt genotype in the contaminating parent. Here, contamination of the mother's DNA by the father's DNA is shown. The fraction of contaminating parent's DNA is v. (B) GroupE SNP VAF density plot in the mother is shown when there is no contamination. (C) GroupE SNP VAF density plot in the mother when there is 25% contamination by the father's DNA. The peak shift is shown with an arrow. (D) True versus estimated value for TrioMix (black circle), VerifyBamID2 (blue square), and GATK4 CalculateContamination (green triangle) for in silico simulated parent DNA contaminated by the other parent's DNA. Estimated values below 10−2.5 are shown on the plot's x-axis.
