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    • Challenging Medically-Relevant Genes Benchmark Set

    Metadata Updated: July 29, 2022

    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 November 29, 2021
    Metadata Updated Date July 29, 2022

    Metadata Source

    Harvested from NIST

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date November 29, 2021
    Metadata Updated Date July 29, 2022
    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/data.json
    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 b2ab1849-b31c-4c63-8bae-0f16f09abb45
    Harvest Source Id 74e175d9-66b3-4323-ac98-e2a90eeb93c0
    Harvest Source Title NIST
    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 fccb0ba3473527651ea6bee234fda01d467c1c32
    Source Schema Version 1.1

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