yunuuuu / clonalneoantigenanalysispipeline

README

This analysis pipeline is designed to run a modified version of PyClone - allowing subclonal copy number states. This analysis relies entirely on PyClone. Therefore, this must be installed and set-up. An excellent set of instructions of how to get this up and running can be found at https://bitbucket.org/aroth85/pyclone/wiki/Home. In addition, the analysis assumes copy number data has been obtained (from, for example, ASCAT, https://www.crick.ac.uk/peter-van-loo/software/ASCAT).

In addition, the analysis requires installation of R, and a number of packages, including gplots; gdata; RColorBrewer; wordcloud; sequenza; bootstrap; boot; plyr.

The analysis pipeline can work as a command line tool. The following input is required:

# The identifier for the patient/sample

# Where do you want to save the output? (this should be a full path)

# Where is the ASCAT copy number data saved? (a full path to a directory)

# What is the mutation table saved? (a full path to a directory)

# Where is PyClone installed, e.g. "/farm/babs/redhat6/software/python-2.7.3/bin/PyClone"

<template.config.yaml> # Where is the pyClone template? (a full path to the file)

<clonalDissectionFunctions.R> # where is the clonalDissectionFunctions.R file located? (a full path to the file)

An example of each and every file can be found at https://bitbucket.org/nmcgranahan/clonalneoantigenanalysispipeline/downloads/ExampleFiles.zip

An example implementation of the script is as follows:

/usr/bin/Rscript ~/Downloads/ExampleFiles/clonalDissectionPyClone.R LMS025 ~/Documents/Work/AnalysisPipeline/ ~/Downloads/ExampleFiles/ASCAT/ ~/Downloads/ExampleFiles/SNV/ /farm/babs/redhat6/software/python/bin/PyClone ~/Downloads/ExampleFiles/template.config.yaml ~/Downloads/ExampleFiles/clonalDissectionFunctions.R

Note, the script assumes there is only one mutation table in the snvDir and also only one segmented copy number table in the ascatDir. For the desired format of these tables, please see the example files.

The output should be produced in a folder named _PyClone_phylo. The results of the analysis will be a table called .clonalDissection.txt. A number of figures will also be produced.

This analysis pipeline was implemented in the paper https://www.ncbi.nlm.nih.gov/pubmed/?term=26940869. If you use this tool, please cite this paper. The results on each tumour used, can be found at: https://bitbucket.org/nmcgranahan/clonalneoantigenanalysispipeline/downloads