Ha Lab Software and Pipelines
See the GavinHaLab GitHub page for the full list of project/code repositories.
Software
Keraon
Probabilistic method to estimate cancer phenotypes mixtures from circulating tumor DNA
De Sarkar & Patton et al. Cancer Discovery, 2022.
ctdPheno
Probablistic method to classify tumor phenotypes from circulating tumor DNA
De Sarkar & Patton et al. Cancer Discovery, 2022.
Griffin
A flexible framework for nucleosome profiling of cell-free DNA
Doebley et al. Nat Commun, 2022.
ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
Adalsteinsson, Ha, Freeman, et al. Nature Communications, 2017.
TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Ha et al. Genome Research, 2014.
Pipelines
Structural Variant linked-read pipeline
Snakemake workflow for structural rearrangement analysis of 10X Genomics linked-read WGS
Viswanathan, Ha, Hoff et al, Cell, 2018.
Copy Number & Structural Variation Pipeline
Snakemake for TitanCNA and Svaba analysis workflow
Meng, Ko et al, JCI Insight, 2023.
ichorCNA targeted panel pipeline
Snakemake for ichorCNA targeted panel sequencing analysis workflow
Schweizer, Ha et al, JCO Precision Oncology, 2020.
TitanCNA linked-read pipeline
Snakemake workflow for TITAN analysis of 10X Genomics WGS
Viswanathan, Ha, Hoff et al, Cell, 2018.