genomics-pipeline

Step 10: Telomere Length Estimation

What This Does

Estimates telomere content from WGS BAM files by quantifying telomeric repeat reads (TTAGGG/CCCTAA). Provides a biological age proxy based on telomere attrition.

Why

Telomere length correlates with cellular aging and is a biomarker for age-related disease risk. Shorter telomeres are associated with cardiovascular disease, cancer predisposition, and reduced lifespan. Comparing telomere content between individuals of similar age provides a relative aging benchmark.

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 \
  -v ${GENOME_DIR}/${SAMPLE}:/data \
  lgalarno/telomerehunter:latest \
  telomerehunter \
    -ibt /data/aligned/${SAMPLE}_sorted.bam \
    -o /data/telomere \
    -p ${SAMPLE} \
    --tumor_only

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

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
• --tumor_only mode is REQUIRED for germline WGS (there is no matched normal sample)
• 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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