DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.

ABSTRACT:

Background

Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.

Findings

Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data.

SUBMITTER: Hanghoj K 

PROVIDER: S-EPMC6474913 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature