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

Olson, Nathan D. ; Wagner, Justin ; McDaniel, Jennifer ; Stephens, Sarah H. ; Westreich, Samuel T. ; Prasanna, Anish G. ; Johanson, Elaine ; Maier, Ezekiel J. ; Boja, Emily and Serang, Omar , et al. (2020)
Abstract
The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets,... (More)
The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants. (Less)
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organization
publishing date
type
Working paper/Preprint
publication status
published
subject
keywords
DNA, variant, short-read sequencing, long-read sequencing, benchmark
publisher
bioRxiv
DOI
10.1101/2020.11.13.380741
language
English
LU publication?
yes
id
5798e0a5-a5ee-4d5f-87ed-c78692ff514c
date added to LUP
2020-12-12 14:12:48
date last changed
2021-12-07 09:10:09
@misc{5798e0a5-a5ee-4d5f-87ed-c78692ff514c,
  abstract     = {{The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.}},
  author       = {{Olson, Nathan D. and Wagner, Justin and McDaniel, Jennifer and Stephens, Sarah H. and Westreich, Samuel T. and Prasanna, Anish G. and Johanson, Elaine and Maier, Ezekiel J. and Boja, Emily and Serang, Omar and Jáspez, David and Lorenzo-Salazar, José M. and Muñoz-Barrera, Adrián and Rubio-Rodríguez, Luis A. and Flores, Carlos and Kyriakidis, Konstantinos and Malousi, Andigoni and Shafin, Kishwar and Pesout, Trevor and Jain, Miten and Paten, Benedict and Chang, Pi-Chuan and Kolesnikov, Alexey and Nattestad, Maria and Baid, Gunjan and Goel, Sidharth and Yang, Howard and Carroll, Andrew and Eveleigh, Robert and Bourgey, Mathieu and Bourque, Guillaume and Li, Gen and MA, ChouXian and Tang, LinQi and DU, YuanPing and Zhang, ShaoWei and Morata, Jordi and Tonda, Raúl and Parra, Genís and Trotta, Jean-Rémi and Brueffer, Christian and Demirkaya-Budak, Sinem and Kabakci-Zorlu, Duygu and Turgut, Deniz and Kalay, Özem and Budak, Gungor and Narcı, Kübra and Arslan, Elif and Brown, Richard and Johnson, Ivan J. and Dolgoborodov, Alexey and Semenyuk, Vladimir and Jain, Amit and Tetikol, H. Serhat and Jain, Varun and Ruehle, Mike and Lajoie, Bryan and Roddey, Cooper and Catreux, Severine and Mehio, Rami and Ahsan, Mian Umair and Liu, Qian and Wang, Kai and Sahraeian, Sayed Mohammad Ebrahim and Fang, Li Tai and Mohiyuddin, Marghoob and Hung, Calvin and Jain, Chirag and Feng, Hanying and Li, Zhipan and Chen, Luoqi and Sedlazeck, Fritz J. and Zook, Justin M}},
  keywords     = {{DNA; variant; short-read sequencing; long-read sequencing; benchmark}},
  language     = {{eng}},
  month        = {{11}},
  note         = {{Preprint}},
  publisher    = {{bioRxiv}},
  title        = {{precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions}},
  url          = {{http://dx.doi.org/10.1101/2020.11.13.380741}},
  doi          = {{10.1101/2020.11.13.380741}},
  year         = {{2020}},
}