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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

jtb114/haplogrep3@sha256:7b28d98a0ffb801977bcc0597941259cf2c4dbe4e89756a9a2c4809c3c9c78de

Pinned by immutable digest — the publisher offers no versioned tags (genepi/haplogrep3 was removed from Docker Hub). Canonical value lives in versions.env.

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:/genome/${SAMPLE}/vcf staphb/bcftools:1.21 \
  bcftools view -r chrM /genome/${SAMPLE}/vcf/${SAMPLE}.vcf.gz -Oz -o /genome/${SAMPLE}/vcf/${SAMPLE}_chrM.vcf.gz

# Step 2: Run haplogrep3
docker run --rm -v ${GENOME_DIR}/${SAMPLE}:/genome/${SAMPLE} jtb114/haplogrep3@sha256:7b28d98a0ffb801977bcc0597941259cf2c4dbe4e89756a9a2c4809c3c9c78de \
  classify \
    --tree phylotree-fu-rcrs@1.2 \
    --input /genome/${SAMPLE}/vcf/${SAMPLE}_chrM.vcf.gz \
    --output /genome/${SAMPLE}/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)