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    • Challenging Medically-Relevant Genes Benchmark Set

    Metadata Updated: September 30, 2025

    CMRG v1.00 of a small variant benchmark and structural variant benchmark focused on 273 challenging medically relevant genes for the Genome in a Bottle (GIAB) sample HG002 (aka Ashkenazi son). These benchmarks were generated from a trio-based hifiasm v0.11 (https://doi.org/10.1038/s41592-020-01056-5) diploid assembly of HG002 using PacBio HiFi reads for HG002 for assembly and partitioning into phased haplotypes using Illumina reads for the parents, HG003 and HG004. This benchmark contains vcfs for small and structural variants along with corresponding benchmark bed files indicating regions that are homozygous reference if they do not have a variant in the vcf. We extensively curated the variant calls, excluding any found to be questionable or errors. This benchmark helps measure performance in important challenging regions, including challenging segmental duplications, regions with complex variants, regions with structural variants, and regions affected by false duplications in GRCh37 or GRCh38. This benchmark is described in https://doi.org/10.1101/2021.06.07.444885.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: See this page for license information.

    Downloads & Resources

    References

    https://doi.org/10.1101/2021.06.07.444885
    https://doi.org/10.1038/s41592-020-01056-5

    Dates

    Metadata Created Date September 30, 2025
    Metadata Updated Date September 30, 2025

    Metadata Source

    Harvested from Commerce Non Spatial Data.json Harvest Source

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date September 30, 2025
    Metadata Updated Date September 30, 2025
    Publisher National Institute of Standards and Technology
    Maintainer
    Identifier ark:/88434/mds2-2475
    Language en
    Data Last Modified 2021-09-29 00:00:00
    Category Bioscience:Genomics
    Public Access Level public
    Bureau Code 006:55
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 2466b711-a459-4c56-9aa0-0a666b7ac596
    Harvest Source Id bce99b55-29c1-47be-b214-b8e71e9180b1
    Harvest Source Title Commerce Non Spatial Data.json Harvest Source
    Homepage URL https://data.nist.gov/od/id/mds2-2475
    License https://www.nist.gov/open/license
    Program Code 006:045
    Related Documents https://doi.org/10.1101/2021.06.07.444885, https://doi.org/10.1038/s41592-020-01056-5
    Source Datajson Identifier True
    Source Hash 9c5dc6f845a0701b66e2aed149296b938e13e12d184ffbd0660d81a0801aa3e7
    Source Schema Version 1.1

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