genomics-pipeline

Step 12: Mitochondrial Haplogroup

What This Does

Determines maternal lineage ancestry from mitochondrial DNA variants. Also screens for pathogenic mtDNA mutations.

Why

Mitochondrial haplogroup reveals deep maternal ancestry and can identify mtDNA disease variants. Some haplogroups have known health associations (e.g., longevity, metabolic traits).

Tool

• haplogrep3 (Medical University of Innsbruck)

Docker Image

genepi/haplogrep3

Command

SAMPLE=your_sample
GENOME_DIR=/path/to/your/data

# Step 1: Extract chrM variants from VCF
docker run --rm -v ${GENOME_DIR}/${SAMPLE}/vcf:/data staphb/bcftools:1.21 \
  bcftools view -r chrM /data/${SAMPLE}.vcf.gz -Oz -o /data/${SAMPLE}_chrM.vcf.gz

# Step 2: Run haplogrep3
docker run --rm -v ${GENOME_DIR}/${SAMPLE}:/data genepi/haplogrep3 \
  classify \
    --input /data/vcf/${SAMPLE}_chrM.vcf.gz \
    --output /data/mito/${SAMPLE}_haplogroup.txt \
    --extend-report

# Output: haplogroup classification with quality score

Interpretation

• Common European haplogroups: H, U, J, T, K, V, W, X
• Output includes quality score (0-1): >0.9 = high confidence
• Discordant variants may indicate heteroplasmy (mixture of mtDNA types)

This site is open source. Improve this page.