Merging bam files
 

According to best practice variant detection if You have multiple sequencing of the same sample from 2 different runs You need to merge bam files prior to realigner/indel realigner/mark duplicates. Is it possible to merge bam files that were already realigned/marked duplicated (per each bam separately) ?

Realignment is performed on a set of reads. If you merge two BAMs and add reads to a locus then realignment is needed. Same goes for marking duplicates or recalibrating bases.