2.2 Ancient DNA

A special case of low-depth sequencing data is sequenced from ancient DNA (aDNA). Often the retrieved material is of such low quantity, that low-depth is not a voluntary - but the only accessible choice.
While aDNA data underlies the same challenges as modern low-depth sequencing, it is additionally composed of short and highly degraded reads which are affected by so-called post-mortem damage (PMD).

PMD damage patterns are typically observed in the form of cytosine deamination towards fragment ends and result in a \(C \rightarrow T\) transition on the affected strand and a \(G \rightarrow A\) transition on the complimentary strand in the amplification steps of library preparation. These deaminations do not occur randomly, but instead are observed much more frequently towards fragment ends. This is due to fragment ends of degraded aDNA being more often single-stranded and thus subject to a much higher rate of deamination.

One common approach to dealing with PMD is to hard-trim the sequencing read-ends which results in the loss of a significant fraction of the data.
Here, we follow a different approach, where PMD patterns are not only inferred from the data but also taken into account during genotype likelihood estimation.