Hello guys,<br>I&#39;m trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I&#39;m running into troubles with the GATK tools in a local installation of Galaxy.<br>

The main problem I have is that merging bam files with the samtools merge tool doesn&#39;t keep read group for each sample, causing &quot;Count Covariates&quot; to crash. The pipeline works fine with a single bam file, but I need to realign at least two files at a time. <br>

Is there a way to set the read group of a merged bam inside Galaxy? Are there plans to include the &quot;merge&quot; 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).<br>

<br>Thanks!<br>Camille<br clear="all"><br>-- <br><font color="#888888">*** <br>Camille Stephan-Otto Attolini, PhD<br>Senior Research Officer, Bioinformatics and Biostatistics unit<br>IRB Barcelona<br>Tel (+34) 93 402 0553</font><br>

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