PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

• DOI: 10.1016/j.xgen.2022.100129
• Publication Date: 2022-04-27T14:31:53Z
• Authors: Nathan D. Olson; Justin Wagner; Jennifer McDaniel; Sarah H. Stephens; Samuel T. Westreich; Anish G. Prasanna; Elaine Johanson; Emily Boja; Ezekiel J. Maier; Omar Serang; David Jáspez; José M. Lorenzo-S...; Adrián Muñoz-Barrera; Luis A. Rubio-Rod...; Carlos Flores; Konstantinos Kyri...; Andigoni Malousi; Kishwar Shafin; Trevor Pesout; Miten Jain; Benedict Paten; Pi-Chuan Chang; Alexey Kolesnikov; Maria Nattestad; Gunjan Baid; Sidharth Goel; Howard Yang; Andrew Carroll; Robert Eveleigh; Mathieu Bourgey; Guillaume Bourque; Gen Li; ChouXian Ma; LinQi Tang; YuanPing Du; ShaoWei Zhang; Jordi Morata; Raúl Tonda; Genís Parra; Jean-Rémi Trotta; Christian Brueffer; Sinem Demirkaya-B...; Duygu Kabakci-Zorlu; Deniz Turgut; Özem Kalay; Gungor Budak; Kübra Narcı; Elif Arslan; Richard Brown; Ivan J. Johnson; Alexey Dolgoborodov; Vladimir Semenyuk; Amit Jain; H. Serhat Tetikol; Varun Jain; Mike Ruehle; Bryan Lajoie; Cooper Roddey; Severine Catreux; Rami Mehio; Mian Umair Ahsan; Qian Liu; Kai Wang; Sayed Mohammad Eb...; Li Tai Fang; Marghoob Mohiyuddin; Calvin Hung; Chirag Jain; Hanying Feng; Zhipan Li; Luoqi Chen; Fritz J. Sedlazeck; Justin M. Zook
• Keywords: Benchmarking; Benchmark (surveying); Identification

The precisionFDA Truth Challenge V2 aimed to assess the state of art variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 call sets for one or more sequencing technologies (Illumina, PacBio HiFi, Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants updated Genome a Bottle benchmark genome stratifications. submissions included numerous innovative methods, graph-based machine learning methods scoring short-read long-read datasets, respectively. With approaches, combining multiple performed particularly well. Recent developments have enabled regions, paving way identification previously unknown clinically relevant variants.