qMule MafFilter

This qMule mode searches the supplied directory for MAF files (.maf extension) and applies QCMG-specific filters to sort the records into 2 MAFs - one containing high confidence calls (more stringent filtering) and the other containing lower confidence calls. This mode only works if your MAF has been generated at QCMG and has the QCMG-specific annotations.

qmule org.qcmg.qmule.MafFilter -i $HOME/maf \
                               -o $HOME/maf/highConfidence.maf \
                               -o $HOME/maf/lowerConfidence.maf \
                               -log $HOME/maf/maf_filter.log

The options can appear in any order except for the 2 output files where the high confidence file must be listed first.

Option                                  Description                            
------                                  -----------                            
-i, --input <directory>                 Directory containing maf files to be filtered
-o, --output <output_file>              High confidence filtered maf file
-o, --output <output_file>              Low confidence filtered maf file
    --log <log_file>                    Mandatory log file
    --loglevel <DEBUG>                  Optional logging level (defaults to INFO)
-h, --help                              Shows this help message.               
-v, --version                           Print version info.