bio-phasing-imputation-reference-panels

Create population sample lists

grep "EUR" samples.txt | cut -f1 > european_samples.txt grep "AFR" samples.txt | cut -f1 > african_samples.txt grep "EAS" samples.txt | cut -f1 > east_asian_samples.txt

Subset reference to specific population

bcftools view -S european_samples.txt
1000GP.chr22.vcf.gz
-Oz -o 1000GP_EUR.chr22.vcf.gz

## Beagle uses VCF directly, but ensure proper format

bcftools view -m2 -M2 -v snps reference.vcf.gz | \
    bcftools annotate --set-id '%CHROM:%POS:%REF:%ALT' | \
    bgzip > reference_beagle.vcf.gz
bcftools index reference_beagle.vcf.gz