GATK RealignerTargetCreator 's input is a normal-tumor bam list,is there any difference in output with put the bam files one by one?why need the co-realign,why not just realignment one by one?
It is to ensure the two BAM files are realigned in the exact same way. Sometimes you may see evidence for an indel in one BAM but not the other. You want all possible indels to be realigned in both BAMs. Have a look at this thread too.
Thank you very much!