#29 · Tools & infrastructure
Computational tools standardize benchmarking and interpretation of variants
The dominant thread is computational interpretation of variant effects, with resources and frameworks that standardize scoring, benchmarking, and consensus. A leakage-controlled benchmark of variant effect predictors yields a gradient-boosting consensus model for single amino acid mutations. MetaDome 2027 aggregates missense population and pathogenic evidence across homologous Pfam domains with GRCh38 support, and MitImpact 4 extends mitochondrial DNA interpretation beyond the 13 protein-coding genes to coding and non-coding variants. Verix harmonizes complex structural variant callsets, CNVision maps intragenic CNV breakpoints to coding sequences, and an in silico framework tests clinical sequencing pipelines against planted truth variants. The new element is breadth: scope moves from coding-sequence missense scoring toward non-coding mtDNA positions and across variant classes.
Published papers
Verix: a toolkit for benchmarking and harmonization of complex structural variants.
Verix is a toolkit for evaluating complex structural variant calls with multi-breakpoint diagnostic metrics and consensus harmonization across callsets and…
MitImpact 4: a genome-wide resource for the interpretation of coding and non-coding mitochondrial DNA variants.
Mitochondrial DNA variants are a frequent cause of inherited disease, yet their computational interpretation has focused almost exclusively on the 13 protein-co
MetaDome 2027: a comprehensively updated resource for aggregating missense variant evidence across homologous human protein domains.
MetaDome 2027 updates a resource aggregating missense variant population and pathogenic evidence across homologous Pfam domains, with GRCh38 support and…
Preprints
CNVision: a computational framework for functional interpretation of intragenic copy number variants
CNVision is a containerized framework that standardizes interpretation of intragenic CNVs, mapping breakpoints to coding sequences and classifying…
Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model
Single amino acid mutations are among the most common forms of genetic variation, with effects ranging from negligible to severe disruption of protein function.
An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings
End-to-end in silico framework testing clinical sequencing pipelines against planted truth variants from reads to reportable findings, with stage-localized…
Topic history
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