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Accelerate HaplotypeCaller step
I am using GATK in a clinical context for NGS diagnosis. The issue is that the HaplotypeCaller take some time, too much time actually (2h per patient).
I tried this things :
- reduce the bam file size by keeping only the genomic regions of my diagnosis genes but it looks like it still run all the hg19 genome.
- ask "only variants" with the output_mode option but the output file is exactly the same than the default one.
- use several CPU thread, but 1 CPU = 147 min, 2 CPU = 89 min, 3 CPU = 80 min. And I don't have this much CPU available so it is not interesting above 2 CPU , and still not fast enough.
I can't use the data thread option right now, would it allow me to gain more time than the CPU option ?
There is the interval option but I don't think it would allow me to gain enough time since I have gene of interest on almost all chromosomes.
I would appreciate to have your guidance regarding this problem. How would you do to make this HaplotypeCaller step faster ?
Many thanks in advance.