Overview of TrioMix. (A) Sequence alignment file in BAM or CRAM format for the father, mother, and offspring is required. A reference FASTA file is also required. A common single nucleotide polymorphism (SNP) position in BED format can be used as an optional input file to restrict the analysis to those sets of SNPs. Reference and alternative read counts (shown as yellow stars) at the SNP loci in the parents are used to infer the genotypes, and read counts in the offspring are used to build a maximum likelihood estimate (MLE) model to identify the source and quantity of the contamination. (B) SNPs are classified into five groups based on their genotypes. Individuals highlighted in gray are the contamination targets investigated in each SNP group. Each group is used to calculate different DNA contamination targets and sources in the mixture.
