Camille, thanks for reporting this - I think you have found a bug.
We definitely need to be able to preserve metadata when we merge bams.
Thanks for your suggestion of using mergeSamFiles - yes, I think it
might be a good fix for this problem - but it will take a little while
and won't reach the Main site for a few weeks once it's done. It is
possible to write your own wrapper locally if you need it fast.
Sorry for the inconvenience and thanks again.
On Wed, Aug 3, 2011 at 6:15 PM, Camille Stephan
> Hello guys,
> I'm trying to run a pipeline of the best practices for snp and indel
> discovery as described by the people at Broad and I'm running into troubles
> with the GATK tools in a local installation of Galaxy.
> The main problem I have is that merging bam files with the samtools merge
> tool doesn't keep read group for each sample, causing "Count Covariates" to
> crash. The pipeline works fine with a single bam file, but I need to realign
> at least two files at a time.
> Is there a way to set the read group of a merged bam inside Galaxy? Are
> there plans to include the "merge" tool from Picard in Galaxy? Is there an
> easy way for me to do this locally? (Although I would like to run this in
> the cloud later on when the workflow is ready).
> Camille Stephan-Otto Attolini, PhD
> Senior Research Officer, Bioinformatics and Biostatistics unit
> IRB Barcelona
> Tel (+34) 93 402 0553
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Ross Lazarus MBBS MPH;
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