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30 datasets found
  1. Challenging Medically-Relevant Genes Benchmark Set

    • data.nist.gov
    • catalog.data.gov
    • +1more
    Updated Sep 29, 2021
  2. PopDel identifies medium-size deletions jointly in tens of thousands of...

    • zenodo.org
    • explore.openaire.eu
    tar
    Updated Feb 1, 2021
    + more versions
  3. f

    Additional file 2 of cDNA-detector: detection and removal of cDNA...

    • springernature.figshare.com
    • figshare.com
    xlsx
    Updated Jun 2, 2023
  4. d

    Telomere dataset used for calculating bulk and chromosome specific telomere...

    • search.dataone.org
    • datadryad.org
    Updated Apr 19, 2024
  5. f

    VCF files of single individual SV merging using PanPop and other SV merger...

    • figshare.com
    application/x-gzip
    Updated Jan 18, 2024
  6. HG002 PacBio Hifi

    • figshare.com
    application/gzip
    Updated Jun 21, 2023
  7. Assembly of human HG002 (GM24385) ONT Q20+ Simplex dataset generated by...

    • zenodo.org
    application/gzip
    Updated Nov 26, 2021
  8. lra-supplemental-HG002-SV.vcf.tar.gz

    • figshare.com
    application/x-gzip
    Updated Nov 15, 2020
  9. f

    HG002 Ultima (2024)

    • figshare.com
    application/gzip
    Updated Apr 5, 2024
  10. HG002

    • figshare.com
    application/gzip
    Updated Dec 6, 2022
  11. Performance of deletion calls for HG002.

    • figshare.com
    xls
    Updated May 31, 2023
  12. Data from: SVXplorer: three-tier approach to identification of structural...

    • zenodo.org
    application/gzip
    Updated Feb 5, 2020
  13. Minigraph pangenome graphs for HPRC year-1 samples

    • zenodo.org
    application/gzip
    Updated Aug 12, 2022
  14. f

    Table_1_stLFRsv: A Germline Structural Variant Analysis Pipeline Using...

    • frontiersin.figshare.com
    xlsx
    Updated Jun 4, 2023
  15. Heuristics used to determine HG002 genotypes.

    • plos.figshare.com
    xls
    Updated May 31, 2023
  16. f

    Additional file 1 of ECNano: A cost-effective workflow for target enrichment...

    • figshare.com
    xlsx
    Updated Jun 2, 2023
  17. f

    HG002 Illumina PCR Free

    • figshare.com
    application/gzip
    Updated Jun 21, 2023
    + more versions
  18. HG002 Ultima (2022)

    • figshare.com
    application/x-gzip
    Updated Apr 5, 2024
  19. Sequencing Genome in a Bottle samples

    • zenodo.org
    bin
    Updated Sep 21, 2023
  20. Human genome assemblies enhanced by LOCLA

    • zenodo.org
    zip
    Updated Aug 29, 2023
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National Institute of Standards and Technology (2021). Challenging Medically-Relevant Genes Benchmark Set [Dataset]. http://doi.org/10.18434/mds2-2475
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Challenging Medically-Relevant Genes Benchmark Set

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2 scholarly articles cite this dataset (View in Google Scholar)
Dataset updated
Sep 29, 2021
Dataset provided by
National Institute of Standards and Technologyhttp://www.nist.gov/
License

https://www.nist.gov/open/licensehttps://www.nist.gov/open/license

Description

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.

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