Using vcftools and got Error: Unknown option: --max-missing
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2.8 years ago
pmiller ▴ 10

Hello, I just installed vcftools and was doing a tutorial to learn more about filtering .vcf files since I have to start doing this soon. The website for the tutorial is: http://www.ddocent.com/filtering/

This is the command I'm running:

vcftools --gzvcf raw.vcf.gz --max-missing 0.5 --mac 3 --minQ 30 --recode --recode-INFO-all --out raw.g5mac3

I don't think there is a problem with the basic installation since I can run all the commands as long as I remove the --max-missing 0.5.

So the following works just fine and produces the output files correctly (but obviously it does not filter out genotypes that occur below 50%).

vcftools --gzvcf raw.vcf.gz --mac 3 --minQ 30 --recode --recode-INFO-all --out raw.g5mac3

I haven't been able to find anything about this being a problem with online searches or checking the vcftools website. I absolutely will need to filter out genotypes based on prevalence in my real file. Does anyone have any suggestions?

vcftools • 1.4k views
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Try bcftools instead. The author of vcftools has ceased updating vcftools for a while.

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