If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
RNA seq TopHat output to variant calls
We are planning to use GATK for snp calling on our RNA-Seq. We mapped our RNA-Seq data using TopHat. The pipeline we are planning to use is the same as the DNA sequencing pipeline:
.bam > filtering (fixmate, remove duplicates, ..) > realignment > recalibration > calling variants
I was wondering if anyone has any suggestions/tips for RNA-Seq SNP calling that we need to consider.
Greatly appreciate your input.