Why do you think it is putting "--max-alleles 20" to "--max-alleles 2"? Is this information explicitly available in the job log?
One more question, if the two VCFtools commands (on UKB RAP vs. outside) are the same, does that mean that you run it in both cases on UKB RAP data? Or you mean the same commands but different input data?
@Megan Ramaker? Seeing only two max alleles could be due to data, other parameters, or different defaults for different version of the tool. On RAP, the vcftools is v0.1.16 without any modification. There is no modification from default vcftools. I would recommend you check into the data or other parameters as the next step. However, if you are convincing that this version of vcftools is problematics, you may request the version update with the RAP team.
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How does your Swiss Army Knife VCFtools command look like? Is this exactly the same command you use outside of DNAnexus?
Yes. I have even tried to use the argument --max-alleles 20 but it defaults to 2 for some reason.
Why do you think it is putting "--max-alleles 20" to "--max-alleles 2"? Is this information explicitly available in the job log?
One more question, if the two VCFtools commands (on UKB RAP vs. outside) are the same, does that mean that you run it in both cases on UKB RAP data? Or you mean the same commands but different input data?
@Megan Ramaker? Seeing only two max alleles could be due to data, other parameters, or different defaults for different version of the tool. On RAP, the vcftools is v0.1.16 without any modification. There is no modification from default vcftools. I would recommend you check into the data or other parameters as the next step. However, if you are convincing that this version of vcftools is problematics, you may request the version update with the RAP team.
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