bio-phasing-imputation-haplotype-phasing

With genetic map (improves accuracy)

java -jar beagle.22Jul22.46e.jar
gt=input.vcf.gz
map=plink.chr22.GRCh38.map
out=phased

## Process each chromosome separately

for chr in {1..22}; do
    java -Xmx16g -jar beagle.jar \
        gt=input.chr${chr}.vcf.gz \
        map=genetic_maps/plink.chr${chr}.GRCh38.map \
        out=phased.chr${chr} \
        nthreads=8
done

## Concatenate chromosomes

bcftools concat phased.chr*.vcf.gz -Oz -o phased.all.vcf.gz
bcftools index phased.all.vcf.gz