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
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Camille Stephan-Otto Attolini, PhD
Senior Research Officer, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0553