RT Journal Article
SR Electronic
T1 xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 295071
DO 10.1101/295071
A1 Jesse Farek
A1 Daniel Hughes
A1 Adam Mansfield
A1 Olga Krasheninina
A1 Waleed Nasser
A1 Fritz J Sedlazeck
A1 Ziad Khan
A1 Eric Venner
A1 Ginger Metcalf
A1 Eric Boerwinkle
A1 Donna M Muzny
A1 Richard A Gibbs
A1 William Salerno
YR 2018
UL http://biorxiv.org/content/early/2018/04/05/295071.abstract
AB Motivation The rapid development of next-generation sequencing (NGS) technologies has lowered the barriers to genomic data generation, resulting in millions of samples sequenced across diverse experimental designs. The growing volume and heterogeneity of these sequencing data complicate the further optimization of methods for identifying DNA variation, especially considering that curated highconfidence variant call sets commonly used to evaluate these methods are generally developed by reference to results from the analysis of comparatively small and homogeneous sample sets.Results We have developed xAtlas, an application for the identification of single nucleotide variants (SNV) and small insertions and deletions (indels) in NGS data. xAtlas is easily scalable and enables execution and retraining with rapid development cycles. Generation of variant calls in VCF or gVCF format from BAM or CRAM alignments is accomplished in less than one CPU-hour per 30× short-read human whole-genome. The retraining capabilities of xAtlas allow its core variant evaluation models to be optimized on new sample data and user-defined truth sets. Obtaining SNV and indels calls from xAtlas can be achieved more than 40 times faster than established methods while retaining the same accuracy.Availability Freely available under a BSD 3-clause license at https://github.com/jfarek/xatlas.Contact farek{at}bcm.eduSupplementary information Supplementary data are available at Bioinformatics online.