hello all,

i am having a hard time in using bcftools set set some variants in my vcf to missing.

as i understand missing2ref is no longer used and replaced with setGT. having said that, it is not clear how to use it.

i need to set any variant with genotype quality (GQ) < 20 to missing. this will require that i use the plugin +fill-tags at the first stage, but then how do i use the setGT plugin? how is the filter command written?

i am so lost here. thanks in advance
    bcftools +setGT in.vcf.gz  -- -t q -n . -i 'FMT/GQ<90' 