Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?