Quickstart

Install

pip install telomerehunter2

Bulk (single sample)

telomerehunter2 \
  -ibt sample.bam \
  -o results/ \
  -p SampleID \
  -b telomerehunter2/cytoband_files/hg19_cytoBand.txt

Bulk (tumor vs control)

telomerehunter2 \
  -ibt tumor.bam \
  -ibc control.bam \
  -o results/ \
  -p PairID \
  -b telomerehunter2/cytoband_files/hg19_cytoBand.txt

Single-cell

telomerehunter2-sc \
  -ibt sc_sample.bam \
  -o results/ \
  -p SampleID \
  -b telomerehunter2/cytoband_files/cytoband.txt \
  --min-reads-per-barcode 10000

Next steps

• See Use cases for common patterns.
• See FAQ for troubleshooting and performance tips.