VCFtools filtering problem

[Nick Bell]

I'm having some issues filtering individuals out with a GQ below a given threshold.

Using the command ./vcftools --vcf AST.txt --minGQ 10 --indv --recode
I get 0 individuals kept.

If I run it without the --indv flag it turns all my genotypes to ./.

Any ideas?

[TiborNagy]

Yes, because you forget to set the parameter for example: --indv NA12878

[Nick Bell]

I realise now that I misinterpreted entirely what the --indv flag meant. I wanted to filter each and every individual by it's quality, not just one!