Haplotype Phasing

Haplotype Phasing

Beagle 5.4 Phasing (Recommended)

# Download Beagle 5.4
wget https://faculty.washington.edu/​browning/​beagle/​beagle.22Jul22.46e.jar

# Basic phasing
java -jar beagle.22Jul22.46e.jar \
    gt=input.vcf.gz \
    out=phased

# Output: phased.vcf.gz (phased genotypes)

# With genetic map (improves accuracy)
java -jar beagle.22Jul22.46e.jar \
    gt=input.vcf.gz \
    map=plink.chr22.GRCh38.map \
    out=phased

Beagle Options

java -jar beagle.22Jul22.46e.jar \
    gt=input.vcf.gz \
    out=phased \
    map=genetic_map.txt \
    nthreads=8 \
    window=40 \
    overlap=4 \
    ne=20000 \              # Effective population size
    seed=12345              # For reproducibility

Phase Per Chromosome

# 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

SHAPEIT5 Phasing (for Large Datasets)

# Phase common variants first
shapeit5_phase_common \
    --input input.vcf.gz \
    --map genetic_map.txt \
    --output phased_common.bcf \
    --thread 8 \
    --log phased.log

# Then phase rare variants
shapeit5_phase_rare \
    --input input.vcf.gz \
    --scaffold phased_common.bcf \
    --map genetic_map.txt \
    --output phased.bcf \
    --thread 8

SHAPEIT5 with Reference Panel

# Improves phasing using reference haplotypes
shapeit5_phase_common \
    --input input.vcf.gz \
    --reference reference_panel.bcf \
    --map genetic_map.txt \
    --output phased.bcf \
    --thread 8

Beagle with Reference Panel

# Use reference panel for better phasing
java -jar beagle.22Jul22.46e.jar \
    gt=input.vcf.gz \
    ref=reference.vcf.gz \
    map=genetic_map.txt \
    out=phased \
    nthreads=8

Input Preparation

# Filter variants before phasing
bcftools view -m2 -M2 -v snps input.vcf.gz -Oz -o biallelic_snps.vcf.gz

# Remove missing genotypes (optional)
bcftools view -g ^miss biallelic_snps.vcf.gz -Oz -o no_missing.vcf.gz

# Normalize (important!)
bcftools norm -f reference.fa -Oz -o normalized.vcf.gz input.vcf.gz

Check Phasing Results

# View phased genotypes (| instead of /)
bcftools query -f '%CHROM\t%POS\t[%GT\t]\n' phased.vcf.gz | head

# Unphased: 0/​1
# Phased: 0|1 or 1|0

# Count phased vs unphased
bcftools query -f '[%GT\n]' phased.vcf.gz | grep -c '|'

Genetic Maps

# Download genetic maps (GRCh38)
wget https://faculty.washington.edu/​browning/​beagle/​genetic_maps/​plink.GRCh38.map.zip
unzip plink.GRCh38.map.zip

# Format: chromosome position rate(cM/​Mb) genetic_position(cM)
# chr1 55550 2.981822 0.000000

Key Parameters

Memory Requirements

Phasing Accuracy Metrics

• Switch error rate: Rate of phase switches vs truth
• Mismatch error rate: Overall haplotype differences
• Measure using trio data or known haplotypes

Related Skills

• phasing-imputation/​genotype-imputation - Impute after phasing
• phasing-imputation/​reference-panels - Get reference data
• variant-calling/​filtering-best-practices - Prepare input VCF
• population-genetics/​linkage-disequilibrium - LD analysis