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Atlas: analysis tools for low-depth and ancient samples

Link, Vivian ; Kousathanas, Athanasios ; Veeramah, Krishna ; Sell, Christian ; Scheu, Amelie ; Wegmann, Daniel

In: bioRxiv, 2017, p. 105346

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...