Data Publication

Challenging Medically-Relevant Genes Benchmark Set

Justin Wagner, Nathan D Olson , Jennifer McDaniel, Justin M Zook
Contact: Nathanael David Olson..
Identifier: doi:10.18434/mds2-2475
Version: 1.0...

Abstract

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.
Research Topics: Bioscience: Genomics    
Subject Keywords: Human genomics, DNA sequencing, Reference materials, Medical genomics, Bioinformatics    

Data Access

These data are public.
Data and related material can be found at the following locations:
  GIAB FTP Site
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About This Dataset

Version: 1.0...
Cite this dataset
Wagner, Justin, Olson, Nathan D, McDaniel, Jennifer, Zook, Justin M (2021), Challenging Medically-Relevant Genes Benchmark Set, National Institute of Standards and Technology, https://doi.org/10.18434/mds2-2475 (Accessed 2022-12-03)
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