Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.

ABSTRACT:

Background

During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods.

Results

We use vg to a

SUBMITTER: Martiniano R 

PROVIDER: S-EPMC7499850 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature