Can I use GATK workflow for plant (Cannabis) to detect variants?
Yes to both of your questions. @SkyWarrior is correct that knowing the ploidy of your plant is important (so you can set it in the variant caller). Other than that, you should be able to use the Best Practices.
For RNA-seq data, we are working on the Best Practice, so they are not fully available yet.
Hi GATK team,
Can I use GATK workflow for plant (RNAseq data) to detect variants? Is there any best practices for plant?
Yes you can. But do you know the ploidy of your samples?
It is a diploid genome (9 autosomes and 1 pair of sex chromosomes). I am working on the transcriptomic data.
First, I am going to do the denovo assembly using Trinity tool. Later on going to do variant calling.
Great, let us know how things work out. You may also find the WDLs in this repository helpful.