A software package for detection of copy number alterations from tumor samples
C++ Perl C Makefile Shell
Switch branches/tags
Nothing to show
Clone or download
Latest commit 10c52b1 May 9, 2015
Permalink
Failed to load latest commit information.
cnv cleaning tumor_purity.pl May 8, 2015
common initial import May 8, 2015
docs Updated download.md May 8, 2015
examples initial import May 8, 2015
.gitignore change makefile May 8, 2015
README.md cleaning tumor_purity.pl May 8, 2015
locations.mk change makefile May 8, 2015
makefile change makefile May 8, 2015
mkdocs.yml add docs May 8, 2015

README.md

PennCNV2

A C++ software package for detection of copy number alterations on tumor samples from SNP arrays and NGS data

PREREQUISITES

You will need to check that the following libraries are available on your system.

These are usually pre-installed on modern linux distributions, and if not, a simple command such as 'yum install gsl-devel' and 'yum install boost-devel' (if YUM is the package manager) will suffice.

BUILDING

You will then want to assign the path of the installations in locations.mk

To compile, run:

make

CONFIGURATION

You will now want to set some optional tuning parameters in the XML file that is directly relevant to the desired analysis. Valid analysis strings are "tumor_cnv" and "seq_cnv". The latter analysis is currently under development.

The XML file must be named .xml (e.g. tumor_cnv.xml for the tumor CNV method).

Tumor CNV configuration

tumor_cnv.xml expects in one of its field a filename that contains a list of signal intensity input files. This manifest file has a header describing the following columns: the path of the input file, a friendly name that will be pre-pended to the results to identify the dataset, and the stromal contamination level of the sample.

Each input file has a header describing the following columns: the SNP identifier, the chromosome (all records must contain the same chromosome), the base pair position (this must be sorted in increasing numerical order), the B allele frequency, and the log2 R ratio.

EXECUTION

You can now execute the program by running

./analyzer

An example is shown in examples directory.