Parliament2: Accurate structural variant calling at scale.

TitleParliament2: Accurate structural variant calling at scale.
Publication TypeJournal Article
Year of Publication2020
AuthorsZarate, S, Carroll, A, Mahmoud, M, Krasheninina, O, Jun, G, Salerno, WJ, Schatz, MC, Boerwinkle, E, Gibbs, RA, Sedlazeck, FJ
Date Published2020 12 21
KeywordsGenome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, Software

BACKGROUND: Structural variants (SVs) are critical contributors to genetic diversity and genomic disease. To predict the phenotypic impact of SVs, there is a need for better estimates of both the occurrence and frequency of SVs, preferably from large, ethnically diverse cohorts. Thus, the current standard approach requires the use of short paired-end reads, which remain challenging to detect, especially at the scale of hundreds to thousands of samples.

FINDINGS: We present Parliament2, a consensus SV framework that leverages multiple best-in-class methods to identify high-quality SVs from short-read DNA sequence data at scale. Parliament2 incorporates pre-installed SV callers that are optimized for efficient execution in parallel to reduce the overall runtime and costs. We demonstrate the accuracy of Parliament2 when applied to data from NovaSeq and HiSeq X platforms with the Genome in a Bottle (GIAB) SV call set across all size classes. The reported quality score per SV is calibrated across different SV types and size classes. Parliament2 has the highest F1 score (74.27%) measured across the independent gold standard from GIAB. We illustrate the compute performance by processing all 1000 Genomes samples (2,691 samples) in

CONCLUSION: Parliament2 provides both a highly accurate single-sample SV call set from short-read DNA sequence data and enables cost-efficient application over cloud or cluster environments, processing thousands of samples.

Alternate JournalGigascience
PubMed ID33347570
PubMed Central IDPMC7751401
Grant ListR03 HD098552 / HD / NICHD NIH HHS / United States
U24 HG010263 / HG / NHGRI NIH HHS / United States
UM1 HG008898 / HG / NHGRI NIH HHS / United States