I am trying to get carriers of high impact variants of DUOX2 with the amazing snpeff/snpsift workflow
snpEff -Xmx64g "hg38" $sample.vcf.gz > $sample_annotated.vcf
I filter keeping variants with high impact in DUOX2
bcftools view $sample_annotated.vcf | SnpSift filter "( EFF[*].IMPACT = 'HIGH' ) & ( EFF[*].GENE = 'DUOX2' )" > $variant_filt.vcf
Now I want to keep only samples that have at least one non-homozygous reference genotype in any of the high impact variants. Is there a way to do this with snpeff or some other tool?