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2.2.9 Quality filtering

The QualFilter split alignment blocks by removing regions with too low quality score. Windows with an average quality below a given threshold will be discarded, and the corresponding block split.


maf.filter=                                 \
    QualFilter(                             \
        species=(species1,species2,etc),    \
        window.size=10,                     \
        window.step=1,                      \
        min.qual=0.8,                       \
        file=data.trash_qual.maf.gz,        \
        compression=gzip),                  \


species=(species1, species2, etc)

A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only. The corresponding sequences must have a quality score line in the original file.


The width, in bp, of the sliding window.


The step by which the window is moved, in bp.


The minimum average quality allowed for each window.


An optional file were removed alignment parts will be stored, in the MAF format. This can be helpful for visual inspection and fine tuning of the filter parameters.


Compression format for output file (if file != none).