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 Vivian Link
A1 Athanasios Kousathanas
A1 Krishna Veeramah
A1 Christian Sell
A1 Amelie Scheu
A1 Daniel Wegmann
YR 2017
UL http://biorxiv.org/content/early/2017/02/02/105346.abstract
AB Summary Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples. Currently, PMD can only be addressed by adjusting sequencing quality scores or by removing potentially damaged data. Here we present ATLAS, a suite of methods to analyze ancient samples that properly account for PMD. It works directly from raw BAM files and contains all necessary methods to infer patterns of PMD, recalibrate base quality scores and accurately genotype ancient DNA, along with many other useful tools. ATLAS enables the building of complete and customized pipelines for the analysis of ancient and low-depth samples in a very user-friendly way. Using 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.