I am trying to run GATK on a whole genome. However my files (8) are in unmapped bam format. So do I have to merge the bam files first (Picard MergeSamFiles) into a single file before using BWA mem and subsequently MergeBamAlignment?
Also according to this tutorial (https://software.broadinstitute.org/gatk/documentation/article?id=6483) even though I have a uBam, I still have to convert it to fastq at an intermediate step. Is this because of Bwa Mem's input constraints?