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.
Question about GATK4 SplitNCigarReads tool
Hi, I used the GATK SplitNCigarReads tools to process RNA-Seq data, which is said to reduce the false positive rate. Then, the processed data was used for SNP calling(by using variant calling tools in GATK). However, after annotating the SNP calling result with GTF file. It shows that only 20%~30% SNP sites locate in the exonic region. I was wonder about it. Ideally, most of the SNP sites may locate in the exonic region. Could u please help me solve this puzzle?