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?
Try bcftools instead. The author of vcftools has ceased updating vcftools for a while.