Personal-Genome-Pipeline

Step 10: Telomere Length Estimation

What This Does

Estimates relative telomere content from WGS BAM files by quantifying telomeric repeat reads (TTAGGG/CCCTAA).

Why

Telomere length correlates with cellular aging at a population level. Comparing telomere content between individuals of similar age, sequenced on the same platform, provides a rough relative comparison. However, telomere length alone is not established as a clinically important standalone risk marker for individuals — it provides only a rough estimate of aging rate and is influenced by many non-age factors (genetics, cell type, technical variables).

Tool

• TelomereHunter (German Cancer Research Center)

Docker Image

lgalarno/telomerehunter:latest

Command

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

docker run --rm --user root \
  --cpus 4 --memory 4g \
  -v ${GENOME_DIR}:/genome \
  lgalarno/telomerehunter:latest \
  telomerehunter \
    -ibt /genome/${SAMPLE}/aligned/${SAMPLE}_sorted.bam \
    -o /genome/${SAMPLE}/telomere/${SAMPLE} \
    -p ${SAMPLE}

# Output: telomere content report in ${GENOME_DIR}/${SAMPLE}/telomere/${SAMPLE}/

TelomereHunter uses -ibt (input BAM tumor) for a single-sample analysis. No --tumor_only flag is needed — when only -ibt is provided (without -ibc for a matched control BAM), TelomereHunter runs in single-sample mode automatically.

Key Metric

• tel_content — GC-corrected telomeric reads per million mapped reads
• Higher values indicate longer/more abundant telomeres
• Compare between samples of known age for relative ranking

Important Notes

• --user root is REQUIRED — Docker container cannot write output files without root permissions
• Short-read WGS (150bp reads) systematically underestimates true telomere length because reads cannot span long repetitive regions
• Results are useful as a relative comparison between samples, NOT as an absolute telomere length measurement
• Long-read sequencing (PacBio/ONT) provides more accurate telomere length if absolute values are needed

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