What parameter would you use for these options (mandatory) in AddOrReplaceReadGroups

LB=String    Read Group Library  Required.
PU=String    Read Group platform unit (eg. run barcode)  Required.
SM=String    Read Group sample name  Required.

Could you please explain these two commands.

Can i use the same rg.txt in my libraries. Or i need to replace them. Not sure by what ?

In second command, why there are two bam ?

I think this solution is invalid.

1. you need to escape @ character, so it would be at least:

   perl -e 'print "\@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n\@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt
   

2. The second problem is that the line defined only the header and -r flag will assign readgroups by filenames - in this case ga and 454. Related question I asked to find a neat solution is here