Quantification of parent DNA contaminated by offspring. (A) GroupD single nucleotide polymorphisms (SNPs) are defined as homo-alt genotypes in the offspring and variant allele frequency (VAF) <1 in the contaminated parent. Here, contamination of the mother by the offspring is shown. The other parent's (father in this case) genotype can either be het or homo-alt. The fraction of offspring contamination is w. (B) A density plot of GroupD SNP VAF in the mother is shown when there is no contamination. (C) A density plot of GroupD SNP VAF in the mother when there is 25% contamination by the offspring's DNA is shown. 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 offspring DNA. Estimated values below 10−2.5 are shown on the plot's x-axis.
