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yes, this is a very small data set just for testing if the pipeline delivers any result. Nevertheless, I think UG should at least detect some SNPs here, shouldn't it?
Hi Geraldine, ok, so then I misunderstood it. I thought this would be used for the confusion matrix. If not, so what does the confusion matrix mentioned in http://gatkforums.broadinstitute.org/discussion/1237 look like? Is it hard coded somewhere…
Ok, tested with fewer thread size (1, 2, 3, 4) and it turns out that your guess was right, @pdexheimer. GATK performance increased with growing thread sizes up to 4 threads. So, to conclude the answers to my questions: 1.) Running GATK with mul…
Hi pdexheimer, I'll try out, thanks for the hint. Currently, I access the data from an SSD drive, so I would expect this to be very performant. Nevertheless, I'll talk to the administration colleagues who set up the system. Also, this would ex…
And I also forgot to mention: I have reads with a length of 250 bp with a coverage of 66 on average...
Hm, wow ok. I'll have to think about that... Another thing I just wanted to mention: When executing GATK with multiple threads, I could always only see a maximum workload of 3 to 4 CPUs used. Could that have to do with the Java VM GATK is running…
Hi Geraldine, yes, I understand that better now. But actually, the files with the increasing data size covered more positions in the genome. I split up the data so that the smallest data set includes all reads covering positions 0 - 25,000,000, t…
I did not see differences between the different permutations of 36 threads. I would have expected that it gets faster when adjusting thread sizes...
Hi Geraldine, I tried several setups for 36 threads, e.g. with -nt 3 and -nct 12, -nt 4 and -nct 8, but none of them speeded up runtime performance.
I should mention that I carried out only SNP calling....
Hi Geraldine, thanks for such an immediate reply! So far, I have ended up at class TraversalEngine from which several other Traversal-classes (TraverseReadsNano?) inherit. I also found the ReadWalkers, but there does not seem to be the code I am…