* Application of whole-genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. * We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded and single-stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments. * Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single-stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content. * Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency.

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