HapCon: estimating contamination of ancient genomes by copying from reference haplotypes.

ABSTRACT:

Motivation

Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches.

Results

We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, wit

SUBMITTER: Huang Y 

PROVIDER: S-EPMC9344841 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature