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

By Nathan Joel Nakatsuka, √Čadaoin Harney, Swapan Mallick, Matthew Mah, Nick Patterson, David Reich

Posted 07 Feb 2020
bioRxiv DOI: 10.1101/2020.02.06.938126 (published DOI: 10.1186/s13059-020-02111-2)

We report a method, ContamLD, for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that contaminants should have haplotypes 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 <10% contamination and data from at least 500,000 sequences covering SNPs). This method is optimized for application to aDNA, leveraging characteristic aDNA damage patterns to provide calibrated contamination estimates. Availability: https://github.com/nathan-nakatsuka/ContamLD. ### Competing Interest Statement The authors have declared no competing interest.

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