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
Tel (+34) 93 402 0553
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