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
<camille.stephan@irbbarcelona.org> wrote:
> 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).
>
> Thanks!
> Camille
>
> --
> ***
> 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;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;