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.
Call variant from RNA-Seq data using Haplotypecaller
My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq data. However, RNA-Seq has different (more complicated) allele frequency. How comes that Haplotypecaller is still being used in RNA-Seq variant calling pipeline? Can anyone share some information on this question? Really appreciated