Jan 17, 2016

svclassify: a method to establish benchmark structural variant calls

BMC Genomics
Hemang ParikhMarc Salit

Abstract

The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). High-quality benchmark small variant calls for the pilot National Institute of Standards and Technology (NIST) Reference Material (NA12878) have been developed by the Genome in a Bottle Consortium, but no similar high-quality benchmark SV calls exist for this genome. Since SV callers output highly discordant results, we developed methods to combine multiple forms of evidence from multiple sequencing technologies to classify candidate SVs into likely true or false positives. Our method (svclassify) calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate SVs as likely true or false positives. We first used pedigree analysis to develop a set of high-confidence breakpoint-resolved large deletions. We then used svclassify to cluster and classify these deletions as well as a set of high-confidence deletions from the 1000 Genomes Project and a set of breakpoint-resolved complex insertions from Spiral Genetics. We find that likely SVs cluster separately from likely non-S...Continue Reading

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  • Citations16
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Citations

Mentioned in this Paper

Depth Perception
Size
Classification
Genome
Synaptic Vesicles
Antimicrobial Susceptibility Breakpoint Determination
Candidate Disease Gene
Gene Deletion
Nucleic Acid Sequencing
Genetic Pedigree

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