GATK variant calling for multiple exome

[sehrrot]

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

[adaptivegenome]

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...

[stuka]

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/wiki/index.php/Parallelism_and_the_GATK#Scatter_.2F_gather_parallelism