About this Dataset

GIAB Benchmarking Of HG002 Assemblies From HPRC Year 1 Bakeoff

The Human Pangenome Reference Consortium (HPRC) tested which combination of current genome sequencing and automated assembly approaches yields the most complete, accurate, and cost-effective diploid genome assemblies with minimal manual curation. Assemblies were generated for GIAB HG002. Variant calls from twenty-nine assemblies were evaluated by NIST using dipcall v0.3 (https://github.com/lh3/dipcall) to produce variant calls when aligned to GRCh38. Benchmarking of small variant calls was then performed against GIAB benchmark v4.2.1 using hap.py v3.12 (https://github.com/Illumina/hap.py).
Organization: Department of Commerce
Last updated: 2025-09-30T05:02:58.592380
Tags: human-genomics-dna-sequencing-reference-materials-genome-assembly-variant-calling-benchmarking-

Tables

Table 1

@usgov.doc_gov_giab_benchmarking_of_hg002_assemblies_from_hpr_589b0b64.table_1

22.29 kB
29 rows
22 columns

CREATE TABLE table_1 (
  "unnamed_0" BIGINT  -- Unnamed: 0,
  "assembly" VARCHAR,
  "snp_recall_ignoregt" DOUBLE,
  "snp_recall" DOUBLE,
  "snp_recall_fullydiploid" DOUBLE,
  "qv_dip_snp" DOUBLE,
  "qv_dip_indel" DOUBLE,
  "qv_dip_snp_indel" DOUBLE,
  "qv_ignoregt_snp_indel" DOUBLE,
  "qv_hap_snp_indel" DOUBLE,
  "nosegdup_qv_dip_snp" DOUBLE,
  "nosegdup_qv_dip_indel" DOUBLE,
  "nosegdup_qv_dip_snp_indel" DOUBLE,
  "segdup_snp_recall" DOUBLE,
  "segdup_snp_recall_ignoregt" DOUBLE,
  "segdup_qv_dip_snp" DOUBLE,
  "segdup_qv_dip_indel" DOUBLE,
  "segdup_qv_dip_snp_indel" DOUBLE,
  "mhc_snp_recall_ignoregt" DOUBLE,
  "mhc_qv_dip_snp" DOUBLE,
  "mhc_qv_dip_indel" DOUBLE,
  "mhc_qv_dip_snp_indel" DOUBLE
);