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Old 04-23-2012, 06:38 PM   #1
sehrrot
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Default GATK variant calling for multiple exome

Hi all,

Currently, I am running Unified genotyper for variant calling for around 100 exomes. It's on the cluster and I found the remaining running time is aournd 3 weeks. Is there any way that I can do within few hours? It's my first time to analyze high-throughput data..

Any advice would be appreciated
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Old 04-23-2012, 10:58 PM   #2
adaptivegenome
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That seems like a long time. Can you share some more details about what you are doing so we can see if there is opportunity for speeding it up? Certainly a generic answer would be to leverage a cloud service to use as much CPU power as you need but I would be interested in learning more about what you are trying to do...
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Old 04-24-2012, 05:09 AM   #3
stuka
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If you have a cluster you might want to look into the scatter/gather parallelism. Basically you do many GATK callings at once spread out around the cluster, with each job just doing a portion of the genomic intervals. Once all jobs are done you merge the results

http://www.broadinstitute.org/gsa/wi...er_parallelism
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