A flexible framework for nucleosome profiling of cell-free DNA
To run Griffin, use the snakemakes in the the 'snakemakes' directory
See the Griffin wiki (https://github.com/adoebley/Griffin/wiki) for further instructions and a demo.
The methodology (corresponding to release v0.2.0) is described in:
Doebley, et al. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. (2022) Nature Communications. doi: https://doi.org/10.1038/s41467-022-35076-w
Release v0.1.0 corresponds to the 2021 preprint in MedRxiv. doi: https://doi.org/10.1101/2021.08.31.21262867
The analysis workflow consists of 3 tasks:
griffin_genome_GC_frequncy
griffin_GC_and_mappability_correction
Calculate the GC bias for a given set of bam files (mappability correction has been turned off by default)
To run this step:
Outputs:
argparse 1.1
pysam 0.15.4
pyBigWig 0.3.17
pandas 1.3.2
numpy 1.21.2
scipy 1.7.1
pyyaml 5.3.1
matplotlib 3.4.1
snakemake 5.5.4
python 3.7.4
Griffin Copyright (c) 2021 Fred Hutchinson Cancer Research Center
All rights reserved.
This program is free software: you can redistribute it and/or modify it under the terms of the BSD-3-Clause-Clear license. No licenses are granted to any patent rights of the Fred Hutchinson Cancer Research Center.
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 BSD-3-Clause-Clear license for more details.
You should have received a copy of the G BSD-3-Clause-Clear license along with this program. If not, see https://spdx.org/licenses/BSD-3-Clause-Clear.html.