MSG: ERROR: No such operator "D"

[BenjaminDEMAILLE]

Hi I try to run filter_vep but I got an error

my command is :

cd  NAS/InfoGene/Rachele/data/VEP_output/

mkdir -p filtered_for_predpathogenic

for chr in {1..22}; do
      filter_vep -i rs_normalized_clean_merged_all_samples_chr${chr}_VEP_output.vcf -filter " (gnomADe_AF <= 0.01 or not gnomADe_AF) and (gnomADg_AF <= 0.01 or not gnomADg_AF)" --only_matched  -o filtered_for_predpathogenic/filter_freq_VEP_filtered_chr_${chr}.vcf
done

for chr in {1..22}; do
      filter_vep -i filter_freq_VEP_filtered_chr_${chr}.vcf -filter "(IMPACT is HIGH or IMPACT is MODERATE)  or (SIFT_score < 0.05 ) or (SIFT_pred is D) or (Polyphen2_HDIV_score > 0.5 ) or (Polyphen2_HDIV_pred is D or Polyphen2_HDIV_pred is P) or (Polyphen2_HVAR_score > 0.5 ) or (Polyphen2_HVAR_pred is D or Polyphen2_HVAR_pred is P) or (LRT_pred  is D) or ( MutationTaster_score > 0.5 ) or  (MutationTaster_pred is A or MutationTaster_pred is D) or (MutationAssessor_pred is H or MutationAssessor_pred is M ) or (FATHMM_score <= -1.5) or (FATHMM_pred is D ) or (PROVEAN_score <= -2.5) or 
(PROVEAN_pred is D) or (MVP_score >= 0.7 ) or ( MPC_score >= 2) or (PrimateAI_score > 0.803) or (PrimateAI_pred is D) or (ClinPred_score > 0.5) or (Aloft_Confidence  is High Confidence ) or (CADD_phred >= 20 ) or (GERP++_RS >= 2)or
(VEST4_score > 0.5) or (MetaSVM_score > 0 ) or (MetaSVM_pred is D) or (MetaLR_score > 0.5) or (MetaLR_pred is D) or (Reliability_index >= 5) or (MetaRNN_score > 0.5) or (MetaRNN_pred is D) or (M-CAP_score > 0.025 )or (M-CAP_pred is D) or (REVEL_score > 0.5)  or (MutPred_score > 0.5 )  or (gMVP_score > 0.7)  or (DEOGEN2_score > 0.5) or (DEOGEN2_pred is D) or (BayesDel_addAF_score > 0.0692655) or (BayesDel_addAF_pred D) or (BayesDel_noAF_score >= -0.0570105 ) or (BayesDel_noAF_pred is D) or
(VARITY_R_score > 0.5) or (VARITY_ER_score > 0.5) or (DANN_score > 0.5) or (fathmm-MKL_coding_score > 0.5)  or (fathmm-MKL_coding_pred is D) or (fathmm-XF_coding_score > 0.5) or (fathmm-XF_coding_pred is D) or (Eigen-raw_coding >= 0.683 ) or (Eigen-PC-raw_coding >= 0.625 ) or
(GenoCanyon_score > 0.5) or (integrated_fitCons_score > 0.5) or (integrated_confidence_value is 0 or integrated_confidence_value  is 1 ) or (LINSIGHT  > 0.5)  or (clinvar_clnsig is Likely_pathogenic or clinvar_clnsig is Pathogenic ) or 
(LIST-S2_score > 0.85 ) or (LIST-S2_pred is D) or  (EVE_score > 0.5) or (EVE_Class10_pred is P ) or (ESM1b_score <  -7.5)  or (ESM1b_pred is D) or (PHACTboost_score > 0.62) or (MutFormer_score > 0.8838) or (MutScore_score > 0.5)" --only_matched  -o filtered_for_predpathogenic/pred_patho_VEP_filtered_${chr}.txt
done

on the second loop

i got :

-------------------- EXCEPTION --------------------
MSG: ERROR: No such operator "D"

STACK Bio::EnsEMBL::VEP::FilterSet::parse_filters /opt/ensembl-vep/modules/Bio/EnsEMBL/VEP/FilterSet.pm:276
STACK Bio::EnsEMBL::VEP::FilterSet::new /opt/ensembl-vep/modules/Bio/EnsEMBL/VEP/FilterSet.pm:139
STACK main::configure /opt/ensembl-vep/filter_vep:136
STACK toplevel /opt/ensembl-vep/filter_vep:52
Date (localtime)    = Fri Oct 11 01:03:30 2024
Ensembl API version = 112
---------------------------------------------------

How can I do ?

[jamie-m-a]

Hi @BenjaminDEMAILLE

It would be handy to have a couple of lines of your VCF to test with - but I suspect it's because 'D' is not a valid thing to match against for most of the instances where you've used it. SIFT should be 'deleterious', for example.