Snakemake workflow for TritonNP

Description

From Triton, the Greek god of waves, and N(ucleosome) P(hasing). This workflow will run TritonNP on matched BAM and (optional) GC-correction files for regions of interest, generating nucleosome phasing metrics and region-level figures as outputs.

This tool has been updated! For the newest version, which now includes fragmentomic analyses, check out: https://github.com/GavinHaLab/Triton . However, if you are looking to reproduce LuCaP PDX phasing analyses from https://doi.org/10.1158/2159-8290.CD-22-0692 you are in the right place.

Contact

Robert Patton

Fred Hutchinson Cancer Center

Contact: rpatton@fredhutch.org

Date: June 21, 2022

Website: https://github.com/denniepatton

Requirements

Software packages or libraries

• Python 3.7.4
  • Snakemake 5.19.2
  • Pysam 0.15.4
  • Argparse 1.1
  • Numpy 1.17.3
  • Pandas 0.25.3
  • Scipy 1.4.1

Scripts

• GenerateFFTFeatures.py (primary tool for extracting phasing features)
• CombinePhasingFM.py (combines output files into a single feature matrix)
• GenerateGCSamples.py (optional; found in config/; used for combining sample info with GC-bias data from Griffin)

Griffin-based GC correction

TritonNP optionally takes BAM-matched GC bias data produced by the Griffin workflow; the workflow with instructions for generating bias files can be found at https://github.com/GavinHaLab/Griffin (when used in the snakemake as opposed to a stand-alone tool GC bias is required).

Sample list

Sample names with paths to matching BAM and GC_bias files should be defined in a YAML file. See PhasingAnalysis/config/samples.yaml for an example. This file may also be generated automatically based on a directory full of BAMs and a path to matched GC_bias files using GenerateGCSamples.py as a stand-alone script.

samples:
  sample_1:
    bam: /path/to/sample_1.bam
    GC_bias: /path/to/sample_1.GC_bias.txt

Snakefiles

1. GenerateFFTFeatures.snakefile

[config.yaml] (PhasingAnalysis/config/config.yaml)

See below for details on [config.yaml] (PhasingAnalysis/config/config.yaml)

Run the analysis

1. Invoking the full snakemake workflow on a cluster using 'slurm'

There is only one file in use for slurm: PhasingAnalysis/config/cluster_slurm.yaml - This file contains memory, runtime, and number of cores for each task. To invoke the snakemake pipeline for qsub:

snakemake -s GenerateFFTFeatures.snakefile --latency-wait 60 --keep-going --cluster-config config/cluster_slurm.yaml --cluster "sbatch -p {cluster.partition} --mem={cluster.mem} -t {cluster.time} -c {cluster.ncpus} -n {cluster.ntasks} -o {cluster.output} -J {cluster.JobName}" -j 40

2. Using the tool as a stand-alone

GenerateFFTFeatures.py may also be run as a stand-alone script to retrieve features of an individual BAM file, with or without GC_bias, on a local machine. Once dependencies are loaded run python GenerateFFTFeatures.py -h (help) to see all available options, which have more detailed explanations below in the configuration and settings section.

Configuration and settings

All (default) settings for the workflow are contained in [config.yaml] (PhasingAnalysis/config/config.yaml), while cluster settings and sample paths are found in PhasingAnalysis/config/cluster_slurm.yaml and PhasingAnalysis/config/samples.yaml, respectively.

sites_bed

Path to BED file containing regions of interest

results_dir

Path to the output directory (default: results)

reference_genome

Path to GRCh38 reference genome for GC calculation (.fa)

plot_list

Text file with a list of region-names to generate plots for (may be left empty)

size_range

Tuple of ints for minimum and maximum fragment sizes to use; defaults to (15, 500)

map_quality

Int defining the minimum read mapping qualilty to keep

Software License

TritonNP Copyright (c) 2022 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.