Hi all,
I am using the GATK 4.0.4.0 for HaplotypeCaller. and i want to run 50 samples in parallel to generate g.vcf. But I can not find the -nct option that available in the old version of GATK, for the GATK 4.0.4.0 version. did something replace -nct in the GATK version 4.0.4.0?
What is the best idea?
This question was previously asked by prasundutta, but I did not get a result and did not find anything (https://gatkforums.broadinstitute.org/gatk/discussion/11304/nct-not-present-in-gatk-4-0-0-0).
Best Regard
Mostafa
I'm having the same problem as reported here. Is the current "solution" still that it's not feasible to parallelize HaplotypeCaller in GATK 4?
And, if there is a way to do it, how?
I've read about Spark but I still don't understand what it is or how to use it.
Please use
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