[Vcftools-help] Unknown option: --geno

[Nandini B <nan...@ho...>]

Hello,

I am trying to run vcftools v0.1.12b to filter my data for the following criteria 1) HWE 2) call rate 3) average genotype quality. The command that is being runned is

vcftools --vcf 00_snps.vcf --hwe 0.005 --geno 0.90 --recode-INFO-all --out 01_snps.indel.vcf

However, the error I get is 'Error: Unknown option: --geno'

What am I missing in my command ? Also, how can I filter my data for average genotype quality or meanGQ ?

Many thanks,