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Old 06-28-2012, 08:09 PM   #4
Senior Member
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

If you are interested check out our pipeline ( Its a qsub based program. We build two flavours. One that reads all the fastq pairs in a folder and aligns then calls variants. The other leverages an input file that allows for proper RG tag assignment that is required for GATK variant calling. Nice thing is it will merge multiple lanes of the same library together for you.
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