How to merge interval files generated from RealignerTargetCreator

golharam

Hi all - I'm using GATK realigner which can take several hours on my samples. I'm trying to optimize my pipeline by dividing this up by chromosome for each node in my cluster. I can call RealignerTargetCreator using the -L parameter for each chromosome which results in a bunch of interval files. Now, I either want to call IndelRealigner using the -L parameter for each chromsome then merge the resulting BAM files, or merge the interval files into one then call IndelRealigner.

1) I don't see a way to merge interval files using GATK. Is this possible?

or

2) Can I call IndelRealigner and process each chromosome separately then merge the resulting BAM files together?

Geraldine_VdAuwera

Comment updated: unfortunately there is a tool called MergeIntervalLists but it's currently not available to the public.

Option #2 is your best bet for now.