I have a vcf file with all genomic sites including invariable, which I generated with the option --ALL-SITES in gatk GenotypeGVCFs. I want to filter that file for quality, coverage etc, but the VCFtools command below excludes all invariant sites. Why? It doesn't seem like it should. I wanna keep them (if they pass filters).
module load vcftools/0.1.14/INTEL-18.0.0 vcftools --gzvcf raw_unfiltered_ALLSITES.vcf --max-missing 0.5 --minQ 30 --minDP 5 --recode --recode-INFO-all --out temp