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.
Using GATK to compare allele frequencies between 2 cohorts
I have RNAseq data for 2 groups of 4 individuals that are phenotypically different. My hypothesis is that some of the genes that show differential expression between the two groups could be due to the presence of snps in exons. Using the RNAseq data, is it possible to use gatk to find differences in snps between these two groups?