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    • precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

    Metadata Updated: July 29, 2022

    The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants. This dataset includes the fastq files provided to participants, the submitted variant callset as vcfs, and the benchmarking results, along with challenge submission metadata.

    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/10.1101/2020.11.13.380741

    Dates

    Metadata Created Date March 11, 2021
    Metadata Updated Date July 29, 2022
    Data Update Frequency irregular

    Metadata Source

    Harvested from NIST

    Other Data Resources

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date March 11, 2021
    Metadata Updated Date July 29, 2022
    Publisher National Institute of Standards and Technology
    Maintainer
    Identifier ark:/88434/mds2-2336
    Data First Published 2020-12-29
    Language en
    Data Last Modified 2021-01-26 00:00:00
    Category Bioscience:Genomic measurements
    Public Access Level public
    Data Update Frequency irregular
    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 d9f50fc1-b2ed-4437-ab83-efa8c56efa57
    Harvest Source Id 74e175d9-66b3-4323-ac98-e2a90eeb93c0
    Harvest Source Title NIST
    Homepage URL https://data.nist.gov/od/id/mds2-2336
    License https://www.nist.gov/open/license
    Program Code 006:045
    Related Documents https://doi.org/10.1101/2020.11.13.380741
    Source Datajson Identifier True
    Source Hash 24bc420f27c78b3e3735fd0b2846041fa2436478
    Source Schema Version 1.1

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