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

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