1000 Genomes

International HapMap Project first data release: ~1 million SNPs in CEU, YRI, and JPT+CHB; produced the first genome-wide LD and recombination maps and drove early GWAS SNP selection and imputation panels.

Expanded SNP density (~3.1M SNPs) and haplotype structure across the same core panels; improved tagging coverage and supported finer-scale association and phasing workflows before large-scale resequencing.

Extended to 11 populations and ~1.6M SNPs; broader ancestry representation and LD maps that informed the design and early phases of the 1000 Genomes Project.

High-coverage whole-genome sequencing of a subset of Phase 3 samples on GRCh38; improves rare-variant discovery, phasing, and structural-variant catalogs while staying aligned with the 1000 Genomes sample framework.

Expanded low-coverage WGS (~1,092 individuals) with exome capture and dense SNP genotyping; primary SNP and indel reference for early imputation panels.

~2,504 individuals across 26 populations; GRCh37/38 VCF releases became the standard allele-frequency, LD, and imputation backbone for GWAS and SV pipelines.

Proof-of-concept low-coverage whole-genome sequencing and SNP arrays across multiple populations; established protocols and data model for the main project.

GRCh37-compatible reference FASTA used across Broad Institute and 1000 Genomes workflows: chromosomes 1-22, X, Y, MT, plus GL/NC unlocalized and unplaced contigs (as in the distributed assembly19 package). Coordinate system matches the 1KG/b37 ecosystem used by many GWAS imputation and joint-calling pipelines.

GRCh37; 1000 Genomes; Broad; b37; reference FASTA

GRCh37 (b37-style) primary chromosomes and contigs plus the hs37d5 decoy sequence set (HuRef/BAC/Fosmid/NA12878-derived sequences) to reduce spurious alignments in short-read mapping. Standard reference for Phase 3-era 1000 Genomes alignment and many imputation and low-pass WGS workflows that target the 1KG coordinate system.

GRCh37; decoy; 1000 Genomes; alignment; hs37d5

GRCh37-based reference FASTA distributed by the 1000 Genomes Project (human_g1k_v37): chromosomes 1-22, X, Y, MT, plus GL unlocalized/unplaced contigs, without separate haplotype scaffolds or EBV. Commonly used as the Phase 1/III alignment reference when harmonizing with public 1KG VCFs and phase panels.

GRCh37; 1000 Genomes; reference FASTA; human_g1k_v37