RT Journal Article
SR Electronic
T1 Benchmarking challenging small variants with linked and long reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.07.24.212712
DO 10.1101/2020.07.24.212712
A1 Justin Wagner
A1 Nathan D Olson
A1 Lindsay Harris
A1 Jennifer McDaniel
A1 Ziad Khan
A1 Jesse Farek
A1 Medhat Mahmoud
A1 Ana Stankovic
A1 Vladimir Kovacevic
A1 Byunggil Yoo
A1 Neil Miller
A1 Jeffrey A. Rosenfeld
A1 Bohan Ni
A1 Samantha Zarate
A1 Melanie Kirsche
A1 Sergey Aganezov
A1 Michael Schatz
A1 Giuseppe Narzisi
A1 Marta Byrska-Bishop
A1 Wayne Clarke
A1 Uday S. Evani
A1 Charles Markello
A1 Kishwar Shafin
A1 Xin Zhou
A1 Arend Sidow
A1 Vikas Bansal
A1 Peter Ebert
A1 Tobias Marschall
A1 Peter Lansdorp
A1 Vincent Hanlon
A1 Carl-Adam Mattsson
A1 Alvaro Martinez Barrio
A1 Ian T Fiddes
A1 Chunlin Xiao
A1 Arkarachai Fungtammasan
A1 Chen-Shan Chin
A1 Aaron M Wenger
A1 William J Rowell
A1 Fritz J Sedlazeck
A1 Andrew Carroll
A1 Marc Salit
A1 Justin M Zook
YR 2021
UL http://biorxiv.org/content/early/2021/10/06/2020.07.24.212712.abstract
AB Genome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here, we use accurate linked reads and long reads to expand the prior benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are not readily accessible to short reads. Our new benchmark adds more than 300,000 SNVs, 50,000 indels, and 16 % new exonic variants, many in challenging, clinically relevant genes not previously covered (e.g., PMS2). For HG002, we include 92% of the autosomal GRCh38 assembly, while excluding problematic regions for benchmarking small variants (e.g., copy number variants and reference errors) that should not have been in the previous version, which included 85% of GRCh38. By including difficult-to-map regions, this benchmark identifies eight times more false negatives in a short read variant call set relative to our previous benchmark.We have demonstrated the utility of this benchmark to reliably identify false positives and false negatives across technologies in more challenging regions, which enables continued technology and bioinformatics development.Competing Interest StatementAMW and WJR are employees and shareholders of Pacific Biosciences. AMB and ITF were employees and shareholders of 10X Genomics. FJS has received sponsored travel from Oxford Nanopore and Pacific Biosciences, and received a 2018 sequencing grant from Pacific Biosciences. AS and VK are employees of Seven Bridges. AC is an employee of Google Inc. and is a former employee of DNAnexus. AF and C-SC are employees of DNAnexus. SMES is an employee of Roche.