I was trying to filter variants in my VCF file based on multiple conditions using filter_vep, specifically focusing on the EAS_AF and gnomADe_EAS_AF values. However, I encountered a strange behavior where, regardless of whether I included the filter: --filter "EAS_AF < 0.01 and gnomADe_EAS_AF < 0.1", the resulting filtered VCF file still contained variants that did not meet these thresholds for EAS_AF and gnomADe_EAS_AF. Here’s the exact command I used:

filter_vep \
  -i $vep_annotation_dir/PIJX2024027.vep.vcf.gz \
  --format vcf \
  --gz \
  -o $vep_annotation_dir/PIJX2024027.filtered.new.vcf \
  --only_matched \
  --filter "EAS_AF < 0.01 or gnomADe_EAS_AF < 0.1" \
  --filter "IMPACT is High or IMPACT is MODERATE" \
  --filter "SIFT is deleterious" \
  --filter "PolyPhen is probably_damaging" \
  --force_overwrite