ContamLD: Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium

Ancient DNA (aDNA) has emerged as a powerful technology for learning about history and biology, but unfortunately it is highly susceptible to contamination. Here we report a method called ContamLD for estimating autosomal aDNA contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that the contaminant should have haplotypes that are uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with