HMMCopy

Overview

HMMCopy is a tool for estimating copy-number profiles from low-coverage (shallow) whole-genome sequencing data. It uses a hidden Markov model to segment normalized read-count data into discrete copy-number states, accounting for GC content and mappability biases. HMMCopy is suited for cost-effective copy-number profiling of cell lines, liquid biopsies, and other samples where deep WGS is impractical.

Used by

• Applied to low-coverage WGS (MiSeq) data from AALE chr_3p-deleted cell clones alongside IchorCNA to detect subclonal copy-number changes during in vitro evolution, including the emergence of subclones with chromosome-3 duplication that rescued the 3p-deletion proliferation defect PMID:29622463

Notes

• Designed for shallow WGS (~0.1–1×); does not require matched normal.
• Requires GC correction and mappability adjustment for accurate segmentation.
• Commonly paired with IchorCNA for tumor-fraction estimation in liquid biopsy applications.

Sources

This page was processed by entity-page-writer on 2026-05-15.