Entering edit mode
3.7 years ago
danson.wooi
•
0
I am very new to this but I was just wondering what commands do people normally use with HaplotypeCaller for variant calling with GATK on RNA-seq data. I am trying to following the pipeline they have established here https://gatk.broadinstitute.org/hc/en-us/articles/360035531192?id=4067 but wasn't too sure of the best set of commands to use.
Consider: A: Inferring genotype based on RNA sequnces