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 (<1x average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1x 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, with mismatches modelled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1x for SNP capture data (1240k) and 0.02x for whole genome sequencing data (WGS), substantially extending the coverage limit of previous male X chromosome based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45,000 and various global ancestries. Availability We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH. Supplementary information Supplementary data are available at Bioinformatics online.

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

“…The nuclear DNA contamination was estimated with several methods. We applied ANGSD 0.934 70 and hapCon 71 for libraries from male individuals, and applied contamLD 72 and a newly developed method that analyses contamination in ROH for female and male libraries (see Supplementary Information, section 2 for a detailed description). The mtDNA contamination was estimated by Schmutzi (--notusepredC --uselength) 69 for all the libraries.…”

Density separation of petrous bone powders for optimized ancient DNA yields

“…We estimated individual library contamination using a recently developed method that requires only 0.02× whole-genome coverage per sample ( Huang and Ringbauer 2021 ). This method models and quantifies mismatches in haploid X Chromosomes as contamination and is therefore restricted to individuals who are molecularly sexed as male, which in our case corresponded to eight out of 10 individuals.…”

“…Duplicated sequences were removed using SAMtools’ rmdup command. Terminal deamination was assessed using mapDamage (v2.0) ( Jónsson et al 2013 ); contamination was assessed on the haploid X Chromosome of males using hapCon with a threshold of 0.02× or 2000 SNPs ( Huang and Ringbauer 2021 ); and molecular sex was determined by looking at the fraction of sequences aligning to the Y Chromosome compared with the total fraction aligning to both sex chromosomes ( Skoglund et al 2013 ). To randomly subsample FASTQ files for reanalysis of merged libraries, seqtk ( ) was used.…”

Demographic history and genetic structure in pre-Hispanic Central Mexico

“…To account for the contamination present in the nuclear DNA, we estimated the contamination with the software hapCon ( 93 ), which is based on detecting polymorphic sites on the X chromosome of male individuals. The estimation of contamination was performed only in three individuals meeting the inclusion criteria (XY assignment and > 0.02x on the X chromosome).…”