Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data
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Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low sequence (ulcWGS) depth < 0.1x to be gained at target loci. Leveraging the recent advances in telomere-to-telomere sequencing of the whole genomes with long reads we show first in a simplified example how short DNA string (k-mer) copy numbers at two different types of repeat arrays correlate with basal chromosome Y (chrY) haplogroups (HG-s). We develop a new k-mer based method Y- mer and show how information from hundreds of thousands of k-mers in distance-based models enables accurate inference of chrY haplogroup from WGS sequence at depth less than 0.01x without additional PCR or capture. We test the performance of Y-mer on ancient DNA and prenatal screening data showing its potential for genetic ancestry inference for cell free, forensic and ancient DNA research from short read WGS data.
