bioRxiv (Cold Spring Harbor Laboratory) · 2017 · 139 citations · 17 references
Life SciencesBioinformaticsGeneticsGenomic Data AnalysisGenomic InformaticsGenomicsAncient DnaAncient Dna GenomicsDegraded Dna AnalysisDna SequencingHigh-throughput GenotypingVariant CallingAncient Dna SequencingAncient GenomicsAncient Human GenomicsBioinformatics Pipelines For GenotypingInference From Ancient DnaPipelines
Abstract 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@unifr.ch Supplementary information Supplementary data are available at Bioinformatics online .
17
The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo, Eric Banks, Ryan Poplin et al. · Nature Genetics · 2011 · 12.4K citations · Full text