from MAF file maf_cpg_filter.py $input $out_file1 $masksite.type #if $masksite.type == "CpG": $masksite.definition #else: "NA" #end if -m $mask_char # $ ^ * ? N CpG sites non-CpG sites Inclusive Restricted numpy

.. class:: infomark **What it does** This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. ----- .. class:: warningmark **Note** *Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species. *Restricted definition* considers sites to be CpG if they are CG in at least one of the species, however, sites that are part of overlapping CpGs are excluded. For more information on CpG site definitions, please refer this article_. .. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565