1000 Genomes Project FUT2 tag SNPs
==================================

This directory holds three-SNP extracts used by examples/run_1kg_*.sh,
examples/run_1kg_assume_trans.sh, and tests. It is not a clinical typing panel.

Source VCFs (not in this repository), under ~/.gwaslab or $GWASLAB_DIR:

  Phase 3 GRCh37 (contig 19):
    {EAS,EUR,AFR}.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
  NYGC 30x GRCh38 (contig chr19):
    {EAS,EUR,AFR}.ALL.split_norm_af.1kg_30x.hg38.vcf.gz

Regenerate with: python examples/extract_1kg.py

Sites:
  rs1047781  se385 (I129F)     GRCh37 19:49206631  GRCh38 19:48703374
  rs601338   se428 (W143X)     GRCh37 19:49206674  GRCh38 19:48703417
  rs602662   se428 LD proxy    GRCh37 19:49206985  GRCh38 19:48703728

IDs in the extracts are CHR:POS:REF:ALT, not rsIDs. genoSecretor matches
markers by coordinates. GT is phased (0|1).

examples/run_1kg_eas.sh prefers GENOSECRETOR_1KG_EAS_VCF, then the full
GWASLab 30x panel, then eas_hg38.vcf.gz here. The EUR/AFR runners do the
same. examples/run_1kg_eas_unphased.sh forces --phase unphased on the EAS
file (--assume-trans is on by default; pass --no-assume-trans to leave
double-hets ambiguous).

Research use only. Genotype-inferred secretor status must not be used for
clinical decision-making.

1000 Genomes Project data: https://www.internationalgenome.org/
