RT Journal Article
SR Electronic
T1 ATLAS: Analysis Tools for Low-depth and Ancient Samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 105346
DO 10.1101/105346
A1 Link, Vivian
A1 Kousathanas, Athanasios
A1 Veeramah, Krishna
A1 Sell, Christian
A1 Scheu, Amelie
A1 Wegmann, Daniel
YR 2017
UL http://biorxiv.org/content/early/2017/03/24/105346.abstract
AB Summary Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamage 2.0.Availability ATLAS is an open-source C++ program freely available at https://bitbucket.org/phaentu/atlas.Contact Daniel.Wegmann{at}unifr.chSupplementary information Supplementary data are available at Bioinformatics online.