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?