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The MaskFilter split alignment blocks by removing regions with too many masked positions (typically showing repeat-content), using sliding windows.
A masked position is identified by a lower case letter in the original sequence.
Windows with more than a given amount of lower case characters will be discarded, and the corresponding block split.
maf.filter= \
[...],
MaskFilter( \
species=(species1,species2,etc), \
window.size=10, \
window.step=1, \
max.masked=2, \
file=data.trash_msk.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.
window.size={int>0}The width, in bp, of the sliding window.
window.step={int>0}The step by which the window is moved, in bp.
max.masked={int>0}The maximum number of lower-case characters allowed in each window.
file={none|{path}}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.
compresion={none|gzip|zip|bzip2}Compression format for output file (if file != none).