Tom, thank you for you answer. You understood my question and phrased it
much better.
The individual .bam files already have @RG tags with LB: and SM: values.
I switched from version 0.1.18 of samtools to version 1.0 and that solved
my problem.
Thanks,
Tommy
On 09/11/2014 20:18, "Thomas W. Blac
Unless I'm completely mistaken, I think the question is "How do I
correctly merge .bam files which already have @RG tags in them, and
their @RG ID values are all the same, even though the files are for
different individuals ?"
If that's the question, then absolutely vanilla samtools merge is
How do I merge bam files with identical @RG IDs? How do I create a merged
output with a unique @RG ID for each unique @RG SM?
The manual reads:
-r Attach an RG tag to each alignment. The tag value is inferred from file
names.
I have tried adding the -r option:
samtools merge -r -R 1:10-100200
