PT  - JOURNAL ARTICLE
AU  - Vivian Link
AU  - Athanasios Kousathanas
AU  - Krishna Veeramah
AU  - Christian Sell
AU  - Amelie Scheu
AU  - Daniel Wegmann
TI  - ATLAS: Analysis Tools for Low-depth and Ancient Samples
AID  - 10.1101/105346
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 105346
4099  - http://biorxiv.org/content/early/2017/03/24/105346.short
4100  - http://biorxiv.org/content/early/2017/03/24/105346.full
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.