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gender mask bed file vs gender map file
In the documentation for SVPreprocess (http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html), there is an advanced parameter -genderMaskBedFile, but in the install test and another documentation page for SVPreprocess (http://gatkforums.broadinstitute.org/discussion/1514/svpreprocess-queue-script), there is a parameter -genderMapFile listed, but no -genderMaskBedFile. Is the difference related to software version or something else? I may be misunderstanding the functions of these parameters and their appropriate files, but if I know the genders of the samples I'm using and specify a genderMapFile, then I do not need to specify a genderMaskBedFile, which would be used to estimate sample gender?