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
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to