Merging multiplexed bam files

Question

[Nikleotide]

Hi,

I have downloaded a dataset from EGA (with the authors permissions of course), but noticed that the files are multiplexed bam files (HiSeq whole genome, HiSeq whole exome, RNASeq.)

What is the easiest way to merge the multiplexed bam files?

Thank you very much in advance.

[Ying W]

why would you want to merge whole genome w/whole exome and RNA-seq?

[Nikleotide]

I don't want to merge RNASeq, WES, and WGS together! For each dataset, I have multiplexed data. For example WES multiplexed and I want to merge them together (merging WES multiplexed together!)

[Ying W]

Could you explain what you mean by multiplexed? I typically see this term used when you have one bam with multiple read groups specifying the different runs/experiments that bam is holding. However, I am confused as how this one bam can be merged... do you mean removing read group information?

Answer 1

[Nikleotide]

This probably should work (I haven't tried it yet since the download is still undergoing.)

Merging Bam Files

I will keep here posted on how it works.