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.
Merging SAM files from different runs to run with GATK
I have a trio, that has been sequenced twice in two different centers. One has a 100b read length and the other 101b read length both illumina fastq files. To get a better coverage I want to merge the SAM files and then pass it to GATK to realign, re-calibrate and call variants. I wonder if someone has done that and/or this is the way to do it?