Welcome to TrioMix’s documentation!
TrioMix is a bioinformatics tool to detect intrafamilial contamination, chimerism, uniparental disomy by investigating inheritance patterns of SNPs. TrioMix quantifies the deviation from Mendelian inheritance patterns by using maximum likelihood esstimation (MLE) inferred from the genotypes of parent-offspring trio. TrioMix can be used on both whole-genome sequencing (WGS) of trios or whole-exome sequencing (WES) of trios.
If you use Triomix in your analysis, please cite our work below.
“Estimation of intrafamilial DNA contamination in family trio genome sequencing using Mendelian inconsistencies. Yoon et al., Genome Research (2022)” [link to paper]
- Basic TrioMix command line: Detection of intrafamilial contamination in the offspring
- TrioMix command line with common SNP only
- Command line arguments
- Default output files
- TrioMix with whole-exome sequencing
- Detection of intrafamilial contamination in the parent (i.e. parent DNA contaminated by child, or by another parent)
- Additional output generated with
- Running TrioMix with a docker image