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.
Is number of samples = 30 enough for variant calling ?
I have 90 exome samples coming from three sample groups. What would be the best idea to do variant calling using GATK? I am planning to call variant from three sample groups separately and and compare them. So, per group there are 30 samples; is this number of sample suffecient enough to merge BAM files and call variants ?
I also have RNASeq data from the same samples. Is it good idea to call variants from RNASeq data too ?