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.
What is a good number of samples that can be used to detect a variant - I have 15K GVCFs with 1000DP
I have 15k GVCFs. To call variants, I understand I can run combineGVCFs step to get batches of GVCF combined. I would like to know whats the good number for a sample set, for bams with coverage of over 800-1000X, to detect a variant? Would the variants called from batches of 500 samples have the same power to detect a variant in all the samples as compared to a variant call in 15k samples together?