Write up Funcotator alpha tutorial for forum

I am available to help in this process @jonn-smith. Just to give you an idea of the evolution of tutorials, here are some example tutorials that focus on somatic CNV calling.

Alpha tutorial that Lee wrote: https://gatkforums.broadinstitute.org/gatk/discussion/7387/description-and-examples-of-the-steps-in-the-acnv-case-workflow
A demo-like tutorial that Sam Lee planned and developed (also Mehrtash was involved so don't be shy about asking around for help) and I encased in writing: https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv/p1
A tutorial to highlight the factors in PoN creation currently used in workshops that I planned, developed and wrote: GATK4_SomaticCNV_worksheet.pdf

Depending on how much responsibility you want to take (I think it nice for you to post a tutorial on the forum under your name for posterity), you can choose to get my review only or have me help in brainstorming, organizing and/or formatting the content.

I have a template available for copy-pasting with formatting elements at https://gatkforums.broadinstitute.org/dsde/discussion/9140/how-to-tutorial-template-a-la-soo-hee-for-copy-pasting#latest. Notice this document is only visible to DSDE members and similarly, you can draft a tutorial in private first then move it to a public forum.

Here are some steps I go through in developing a tutorial. You may choose to skip certain elements, e.g. example data. I have to say that having example data really helps the users.

Find small test data to illustrate important features of the tool; ensure data is publically sharable
Write out commands that include recommended parameters
Explain the important parameters and the impact of changing them
Illustrate with results and screenshots
Get reviewed early by others and incorporate changes
A section of links to related or helpful docs

broadinstitute / gatk

Write up Funcotator alpha tutorial for forum #3774