ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing (ULP-WGS, 0.1x coverage). This is a version maintained by the laboratory of Gavin Ha.
- WDL pipleine
- The WDL pipeline uses release ichorCNA:v0.5.0
- The docker image
gavinhalab/ichorcna:1.0.0can be found at DockerHub - Clone WDL pipleine
- To run the WDL pipeline, please follow instructions here
- Snakemake pipeline
- The Snakemake pipeline is part of release ichorCNA:v0.4.0
- Clone ichorCNA:v0.4.0 or download v0.4.0.tar.gz
- To run the Snakemake pipeline, please follow instructions here
ichorCNA uses a probabilistic model, implemented as a hidden Markov model (HMM), to simultaneously segment the genome, predict large-scale copy number alterations, and estimate the tumor fraction of a ultra-low-pass whole genome sequencing sample (ULP-WGS).
The methodology and probabilistic model are described in:
Adalsteinsson, Ha, Freeman, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017) Nature Communications Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y
The analysis workflow consists of 2 tasks:
- GC-content bias correction (using HMMcopy)
a. Computing read coverage from ULP-WGS
b. Data correction and normalization - CNA prediction and estimation of tumor fraction of cfDNA
If you have any questions or feedback, please contact us at:
Email: gha@fredhutch.org or pchandra@fredhutch.org
ichorCNA is maintained by Gavin Ha, Pooja Chandra, and Michael Yang.
ichorCNA was originally developed in collaboration with
- Blood Biopsy Group, Group Leader Viktor Adalsteinsson, Broad Institute of MIT and Harvard
- Laboratory of Matthew Meyerson, Medical Oncology, Dana-Farber Cancer Institute
- Laboratory of J. Christopher Love, Koch Institute for integrative cancer research at MIT
- Laboratory of Gad Getz, Cancer Program, Broad Institute
ichorCNA Copyright (C) 2024 Gavin Ha Lab
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.