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.
GATK gtf file
I am using human_g1k_v37.fasta from GATK as a reference file for my Targeted Sequence Analysis.
I am using Homo_sapiens.GRCh37.75.gtf for making my interval file.
I understand there are a few differences between NCBI fasta sequence and the fasta by GATK.
Is there a gtf file from GATK that can is compatible with the fasta file provided by GATK.