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/2017/02/02/105346.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.