1000 Genomes EAS¶

Four ABO tag SNPs from the 1000 Genomes 30x EAS panel (NYGC, GRCh38, chr9, phased).

Research use only

This extract is a software sanity check, not serology. Genotype-inferred ABO groups must not be used for transfusion or clinical decision-making.

The runner prefers, in order: GENOABO_1KG_EAS_VCF, ~/.gwaslab/EAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz (full indexed panel), then the bundled extract examples/data/1kg_eas/abo_markers.vcf.gz.

See examples/data/1kg_eas/README.txt for panel provenance and marker sites.

Phase auto (default)¶

#!/usr/bin/env bash
# Run genoABO on 1000 Genomes 30x EAS (hg38): full local panel if present, else bundled extract.
# Uses --phase auto (detects phased GT).
set -euo pipefail
ROOT="$(cd "$(dirname "$0")" && pwd)"
# shellcheck source=_1kg_eas_input.sh
source "$ROOT/_1kg_eas_input.sh"

mkdir -p "$ROOT/out"
echo "Using: $VCF"
genoabo "$VCF" \
  --build hg38 \
  --method auto \
  --phase auto \
  -o "$ROOT/out/1kg_eas"
echo "Open: $ROOT/out/1kg_eas.report.html"

./examples/run_1kg_eas.sh

Under --method auto --phase auto this extract yields:

ABO_group	n	percent
O	194	38.5%
B	142	28.2%
A	133	26.4%
AB	35	6.9%

504 samples; all four markers found; diplotypes A/A 20, A/O 113, B/B 18, B/O 124, A/B 35, O/O 194; zero unknown/ambiguous. Counts are a software sanity check, not a population frequency claim.

Example report¶

Snapshot of PREFIX.report.html from the bundled extract (--method auto --phase auto). Research demo, not clinical typing.

Open full report

Forced unphased¶

--phase unphased uses the same VCF but ignores | phase. Default --assume-bo assigns double heterozygotes (O_DEL/NON_O × A/B) to B/O, so group counts match the phased run (A 133, B 142, AB 35, O 194). All 504 calls are phase_mode=unphased (confidence medium). Pass --no-assume-bo to leave those 124 samples ambiguous.

#!/usr/bin/env bash
# Same 1000 Genomes 30x EAS VCF as run_1kg_eas.sh, but ignore phase (--phase unphased).
# The file is still phased (0|1); this run treats it as unphased genotypes.
set -euo pipefail
ROOT="$(cd "$(dirname "$0")" && pwd)"
# shellcheck source=_1kg_eas_input.sh
source "$ROOT/_1kg_eas_input.sh"

mkdir -p "$ROOT/out"
echo "Using: $VCF (forced unphased)"
genoabo "$VCF" \
  --build hg38 \
  --method auto \
  --phase unphased \
  -o "$ROOT/out/1kg_eas_unphased"
echo "Open: $ROOT/out/1kg_eas_unphased.report.html"

./examples/run_1kg_eas_unphased.sh

ABO_group	n (default `--assume-bo`)	n (`--no-assume-bo`)
O	194	194
A	133	133
AB	35	35
B	142	18 (B/B only)
ambiguous	0	124

Counts are a software check, not a population frequency claim.

Sample-level concordance of those 124 double-hets with phased B/O, and the same check in AFR/AMR/EUR, is in 1000 Genomes --assume-bo check.