I am looking into selecting some regions from the exomes VCFs and annotating the variants with CADD and gnomAD.
Outside RAP, this is a trivial task with VEP and plugins, but I wanted to know the best approach within RAP. I could not find a relevant tutorial.
Note: I have dx installed locally.
I personally use https://opencravat.org. If you are interested, I could pass you a notebook that enables it, and I have heard that the developers (JHU) are working on an applet that will work on the RAP.
Comments
3 comments
@Ben Busby? might be able to help. He is very familiar with annotation.
Hi @David John Green? !
I personally use https://opencravat.org. If you are interested, I could pass you a notebook that enables it, and I have heard that the developers (JHU) are working on an applet that will work on the RAP.
Ben
OpenCRAVAT that Ben suggested is great.
As an alternative, if you need to use VEP, you can write your own custom app(let) as described here:
https://documentation.dnanexus.com/developer/apps/intro-to-building-apps
https://documentation.dnanexus.com/developer/apps/developing-spark-apps
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