Article

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

2019-09-26

Abstract excerpt

<h4>Background</h4> 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 ar...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 1d9882f7-defb-5486-807f-55013cd3f6e2
DOI: 10.1101/782755

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graphDOI 10.1101/782755Read

Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome dataSemantic proximity Read

Systematic benchmark of ancient DNA read mapping.Semantic proximity Read

The presence and impact of reference bias on population genomic studies of prehistoric human populationsSemantic proximity Read

Sequence variation aware genome references and read mapping with the variation graph toolkitSemantic proximity Read

Improving ancient DNA read mapping against modern reference genomes.Semantic proximity Read

Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.Semantic proximity Read

Genome GraphsSemantic proximity Read

Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasetsSemantic proximity Read

A catalog of ancient proxies for modern genetic variantsSemantic proximity Read

Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study.Semantic proximity Read

Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genomeSemantic proximity Read

A complete pedigree-based graph workflow for rare candidate variant analysis.Semantic proximity Read