A C++ software package for detection of copy number alterations on tumor samples from SNP arrays and NGS data
You will need to check that the following libraries are available on your system.
- GNU C compiler (gcc/g++)
- GNU scientific library (http://www.gnu.org/software/gsl/)
- Boost C++ libraries (http://www.boost.org)
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.
You will then want to assign the path of the installations in locations.mk
To compile, run:
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.
You can now execute the program by running
An example is shown in examples directory.