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.

Stromal contamination prediction

tumor_purity.pl is a Perl script that can be used to predict the fraction of tumor cells within the sample.

The required input includes a signal intensity file (text file with SNP, Chr, Position, Log R Ratio and B Allele Freq) and a HMM file:

     tumor_purity.pl [arguments] <input-signal-file> <PennCNV-HMM-file>

     Optional arguments:
            -v, --verbose                   use verbose output
            -h, --help                      print help message
            -m, --man                       print complete documentation
                --snpposfile <file>         a file with chr/position information for markers
                --bin <int>                 the BIN for grouping SNPs together (default: 100)
                --grid <int>                the GRID for precision of estimate (default: 50)
                --portion <float>           portion of LRR windows for estimation (default: 0.5)

     Function: calculate tumor purity (1-stromal contamination) levels from signal intensity file with LRR/BAF values

     Example: tumor_purity.pl signal.txt hhall.hmm

An example is shown below that illustrate the strong correlation between predicted stromal contamination and experimental values.


CNA detection

You can now execute the program by running

./analyzer <analysis string>

An example is shown in examples directory.