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.

Variant detection in RNAseq: when to merge samples

jahneldarjahneldar NorwayMember
edited April 2017 in Ask the GATK team

Hi, I have followed the recommendations for my RNAseq variant search as outlined here:
http://gatkforums.broadinstitute.org/gatk/discussion/4067/best-practices-for-variant-discovery-in-rnaseq

Since I am pretty new to the gatk world, silly questions are bound to emerge. Anyway, I have followed the linked Best Practice and are in the process of doing BaseRecalibration now. I have treated my four lines individually, meaning that alle the processes so far have been done individual by individual. My question is whether I have done this correctly - by treating the individuals separately up to now?
Since I am looking for snps, I assume that at one stage I need to merge them together, but should I have done that at an earlier stage?

Feedback/comments are greatly appreciated.
Thank you.

jahn

Post edited by jahneldar on

Answers

Sign In or Register to comment.