Challenging Medically-Relevant Genes Benchmark Set

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.

Resources

Name Format Description Link
5 HG002_GRCh38_CMRG_SV_v1.00.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz.tbi
19 HG002-v0.11.mat.gff.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/hifiasm-assembly/HG002-v0.11.mat.gff.gz
5 HG002v11-align2-GRCh37.hap1.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.hap1.bam
5 HiCanu_2.1_HG002_GRCh37_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_FPs_repeatexpanded_slop50.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/HiCanu_2.1_HG002_GRCh37_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_FPs_repeatexpanded_slop50.bed
0 https://doi.org/10.18434/mds2-2475
0 Github repository with code used to generate benchmark sets. https://github.com/usnistgov/giab-cmrg-benchmarkset
5 HG002_GRCh37_CMRG_smallvar_v1.00.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SmallVariant/HG002_GRCh37_CMRG_smallvar_v1.00.bed
5 HG002_GRCh37_CMRG_SV_v1.00.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/StructuralVariant/HG002_GRCh37_CMRG_SV_v1.00.bed
5 HG002v11-align2-CHM13v1.0.hap1.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.hap1.bam
19 HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SmallVariant/HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.vcf.gz
19 HG002v11-align2-CHM13v1.0.dip.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.dip.vcf.gz
19 HG002_GRCh37_CMRG_smallvar_v1.00.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SmallVariant/HG002_GRCh37_CMRG_smallvar_v1.00.vcf.gz
5 HG002_GRCh37_CMRG_SV_v1.00.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/StructuralVariant/HG002_GRCh37_CMRG_SV_v1.00.vcf.gz.tbi
5 HG002_GRCh38_CMRG_smallvar_v1.00.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SmallVariant/HG002_GRCh38_CMRG_smallvar_v1.00.bed
19 HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SmallVariant/HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz
5 HG002v11-align2-GRCh37.dip.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.dip.bed
19 HG002v11-align2-GRCh37.dip.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.dip.vcf.gz
5 HG002v11-align2-GRCh37.dip.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.dip.vcf.gz.tbi
5 HG002v11-align2-GRCh37.hap1.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.hap1.bam.bai
5 GRCh38_hifiasm_error.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_hifiasm_error.bed
5 HG002_GRCh38_CMRG_SV_v1.00.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.bed
19 HG002_GRCh38_CMRG_SV_v1.00.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz
5 GRCh38_CMRG_benchmark_gene_coordinates.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/GRCh38_CMRG_benchmark_gene_coordinates.bed
5 HG002v11-align2-GRCh38.hap1.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.hap1.bam
5 HG002v11-align2-GRCh38.hap2.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.hap2.bam
5 HG002v11-align2-GRCh38.hap2.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.hap2.bam.bai
5 chksum.md5 https://data.nist.gov/od/ds/ark:/88434/mds2-2475/chksum.md5
5 GRCh37_MRG_GAPs.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh37_MRG_GAPs.bed
5 GRCh37_curation_medicalgene_SV_errorsorunsure.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh37_curation_medicalgene_SV_errorsorunsure.bed
5 GRCh37_hifiasm_error.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh37_hifiasm_error.bed
5 GRCh37_mrg_full_gene.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh37_mrg_full_gene.bed
5 GRCh38_CD4_gaps.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_CD4_gaps.bed
5 GRCh38_CD4_gaps_slop50.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_CD4_gaps_slop50.bed
5 GRCh38_MRG_GAPs.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_MRG_GAPs.bed
5 GRCh38_curation_medicalgene_SV_errorsorunsure_repeatexpanded.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_curation_medicalgene_SV_errorsorunsure_repeatexpanded.bed
19 HG002-v0.11.mat.fa.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/hifiasm-assembly/HG002-v0.11.mat.fa.gz
19 HG002-v0.11.pat.fa.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/hifiasm-assembly/HG002-v0.11.pat.fa.gz
19 HG002-v0.11.pat.gff.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/hifiasm-assembly/HG002-v0.11.pat.gff.gz
47 README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2475/README.md
5 HG002v11-align2-CHM13v1.0.hap2.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.hap2.bam
5 HG002v11-align2-GRCh38.dip.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.dip.bed
19 HG002_GRCh37_CMRG_SV_v1.00.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/StructuralVariant/HG002_GRCh37_CMRG_SV_v1.00.vcf.gz
5 HG002v11-align2-CHM13v1.0.hap2.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.hap2.bam.bai
5 HG002v11-align2-CHM13v1.0.dip.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.dip.vcf.gz.tbi
5 HG002v11-align2-GRCh38.hap1.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.hap1.bam.bai
5 GRCh38_curation_medicalgene_smallvar_complexrepeat_errorsorunsure_repeatexpanded.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_curation_medicalgene_smallvar_complexrepeat_errorsorunsure_repeatexpanded.bed
0 NCBI Hosted Genome In A Bottle FTP Site https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/
0 Github repository with code used to generate figures and perform analysis for manuscript. https://github.com/usnistgov/cmrg-benchmarkset-manuscript
5 HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SmallVariant/HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.vcf.gz.tbi
5 HG002v11-align2-GRCh37.hap2.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.hap2.bam.bai
5 HiCanu_2.1_HG002_GRCh38_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_FPs_repeatexpanded_slop50.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/HiCanu_2.1_HG002_GRCh38_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_FPs_repeatexpanded_slop50.bed
5 GRCh37_CMRG_benchmark_gene_coordinates.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/GRCh37_CMRG_benchmark_gene_coordinates.bed
5 HG002v11-align2-CHM13v1.0.hap1.bam.bai https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.hap1.bam.bai
5 HG002v11-align2-GRCh37.hap2.bam https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SupplementaryFiles/HG002v11-align2-GRCh37/HG002v11-align2-GRCh37.hap2.bam
19 HG002v11-align2-GRCh38.dip.vcf.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.dip.vcf.gz
5 HG002v11-align2-GRCh38.dip.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SupplementaryFiles/HG002v11-align2-GRCh38/HG002v11-align2-GRCh38.dip.vcf.gz.tbi
5 GRCh37_curation_medicalgene_smallvar_complexrepeat_errorsorunsure_repeatexpanded.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh37_curation_medicalgene_smallvar_complexrepeat_errorsorunsure_repeatexpanded.bed
49 combined%20curation%20responses%20from%20benchmarking%20with%20sm%20variant%20v0.02.03%20-%20GRCh37andGRCh38.tsv https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/combined%20curation%20responses%20from%20benchmarking%20with%20sm%20variant%20v0.02.03%20-%20GRCh37andGRCh38.tsv
5 HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SmallVariant/HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.bed
5 HG002_CHM13_CMRG_smallvar_v1.00_GRCh38-equiv-regions_draft.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002_CHM13_CMRG_smallvar_v1.00_GRCh38-equiv-regions_draft.bed
5 HG002v11-align2-CHM13v1.0.dip.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/CHM13v1.0/SupplementaryFiles/HG002v11-align2-CHM13v1.0/HG002v11-align2-CHM13v1.0.dip.bed
5 HG002_GRCh37_CMRG_smallvar_v1.00.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh37/SmallVariant/HG002_GRCh37_CMRG_smallvar_v1.00.vcf.gz.tbi
5 GRCh38_mrg_full_gene.bed https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/GRCh38_mrg_full_gene.bed
5 HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz.tbi https://data.nist.gov/od/ds/ark:/88434/mds2-2475/benchmark_sets/GRCh38/SmallVariant/HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz.tbi
47 HiCanu_2.1_HG002_GRCh38_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_subtract_FPs_repeatexpanded_slop50_manual_curation_sites.tsv_manual_curation_sites.txt https://data.nist.gov/od/ds/ark:/88434/mds2-2475/dependencies/HiCanu_2.1_HG002_GRCh38_difficult_medical_gene_smallvar_benchmark_v0.02.03_intersected_subtract_FPs_repeatexpanded_slop50_manual_curation_sites.tsv_manual_curation_sites.txt

Tags

  • medical-genomics
  • dna-sequencing
  • reference-materials
  • human-genomics
  • bioinformatics

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