CombineGVCFs performance
Posted in Ask the GATK team | Last updated on


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I've got 300 gvcfs as a results of a Queue pipeline, that I want to combine. When I run CombineGVCFs (GATK v3.1-1) this however seems fairly slow:

INFO  15:24:22,100 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
INFO  15:57:52,778 ProgressMeter -      1:11456201        1.10e+07   33.5 m        3.0 m      0.4%         6.4 d     6.3 d 
INFO  15:58:52,780 ProgressMeter -      1:11805001        1.10e+07   34.5 m        3.1 m      0.4%         6.4 d     6.3 d 
INFO  15:59:52,781 ProgressMeter -      1:12140201        1.20e+07   35.5 m        3.0 m      0.4%         6.4 d     6.3 d 

Is there a way of improving the performance of this merge? 6 days seems like a lot, but of course not unfeasible. Likewise, what kind of performance could I expect in the GenotypeGVCFs step?


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