Question: Speed up GATK joint genotype calling?
0
gravatar for jtwalker
3.1 years ago by
jtwalker20
jtwalker20 wrote:

I'm using GATK's GenotypeGVCFs tool to jointly genotype ~1000 samples. It's my understanding that because of the genome wide annotations that are calculated, I can't speed things up by using CombineVCFs on smaller jointly called groups. Am I correct?

Is there some way to speed up my joint genotyping with GATK?

Thanks!

edit: The reference genome we're using is only composed of scaffolds. We're worried that because our genome is only composed of scaffolds that this might be slowing things down. Is this thinking correct, or does GATK not care?

joint genotyping gatk • 1.9k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by jtwalker20

you can also parallelize things using each contig and the option -L

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum131k
0
gravatar for Medhat
3.1 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

Parallelism options

This tool can be run in multi-threaded mode using this option.

TreeReducible (-nt)
  

for more details -nt

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Medhat8.8k

I had considered this, but the gatk doc says that we'd need to have the same amount of ram available for each thread. As our ram usage is already a concern, would this still be a viable option?

ADD REPLYlink written 3.1 years ago by jtwalker20

The idea of threading is that all threads shares the same amount of memory (in contrast to multiprocessing), So my expectation that it should be Ok.

ADD REPLYlink written 3.1 years ago by Medhat8.8k
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