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+split-vep returns ambiguous key errors #1508

Closed JannahS closed 3 years ago

JannahS commented 3 years ago

I have a huge list of CSQ fields and I tried to extract all of them from VEP annotated VCF into tab seperated fields using

bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab input.vcf

I'm getting error below: Note: ambiguous key %AF; using the AF subfield of CSQ, not the INFO/AF tag Error: no such tag defined in the VCF header: INFO/pos

I think this is because there are two AF tags in my VCF. One is the AF tag ##INFO=<ID=AF; and another one is the AF in CSQ field from VEP.

How do I include both AF or skip the ##INFO=<ID=AF so that I can extract all CSQ fields?

Thanks in advance for your help

pd3 commented 3 years ago

Can you show the full VCF header please?

JannahS commented 3 years ago

Full headers are too long, but here are the headers for INFO column in my vcf. 

##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">
##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|REFSEQ_MATCH|SOURCE|REFSEQ_OFFSET|GIVEN_REF|USED_REF|BAM_EDIT|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|REVEL|TSSDistance|MES-NCSS_downstream_acceptor|MES-NCSS_downstream_donor|MES-NCSS_upstream_acceptor|MES-NCSS_upstream_donor|MES-SWA_acceptor_alt|MES-SWA_acceptor_diff|MES-SWA_acceptor_ref|MES-SWA_acceptor_ref_comp|MES-SWA_donor_alt|MES-SWA_donor_diff|MES-SWA_donor_ref|MES-SWA_donor_ref_comp|MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref|SpliceAI_pred_DP_AG|SpliceAI_pred_DP_AL|SpliceAI_pred_DP_DG|SpliceAI_pred_DP_DL|SpliceAI_pred_DS_AG|SpliceAI_pred_DS_AL|SpliceAI_pred_DS_DG|SpliceAI_pred_DS_DL|SpliceAI_pred_SYMBOL|miRNA|1000Gp3_AC|1000Gp3_AF|1000Gp3_AFR_AC|1000Gp3_AFR_AF|1000Gp3_AMR_AC|1000Gp3_AMR_AF|1000Gp3_EAS_AC|1000Gp3_EAS_AF|1000Gp3_EUR_AC|1000Gp3_EUR_AF|1000Gp3_SAS_AC|1000Gp3_SAS_AF|ALSPAC_AC|ALSPAC_AF|APPRIS|Aloft_Confidence|Aloft_Fraction_transcripts_affected|Aloft_pred|Aloft_prob_Dominant|Aloft_prob_Recessive|Aloft_prob_Tolerant|AltaiNeandertal|Ancestral_allele|BayesDel_addAF_pred|BayesDel_addAF_rankscore|BayesDel_addAF_score|BayesDel_noAF_pred|BayesDel_noAF_rankscore|BayesDel_noAF_score|CADD_phred|CADD_phred_hg19|CADD_raw|CADD_raw_hg19|CADD_raw_rankscore|CADD_raw_rankscore_hg19|ClinPred_pred|ClinPred_rankscore|ClinPred_score|DANN_rankscore|DANN_score|DEOGEN2_pred|DEOGEN2_rankscore|DEOGEN2_score|Denisova|ESP6500_AA_AC|ESP6500_AA_AF|ESP6500_EA_AC|ESP6500_EA_AF|Eigen-PC-phred_coding|Eigen-PC-raw_coding|Eigen-PC-raw_coding_rankscore|Eigen-phred_coding|Eigen-raw_coding|Eigen-raw_coding_rankscore|Ensembl_geneid|Ensembl_proteinid|Ensembl_transcriptid|ExAC_AC|ExAC_AF|ExAC_AFR_AC|ExAC_AFR_AF|ExAC_AMR_AC|ExAC_AMR_AF|ExAC_Adj_AC|ExAC_Adj_AF|ExAC_EAS_AC|ExAC_EAS_AF|ExAC_FIN_AC|ExAC_FIN_AF|ExAC_NFE_AC|ExAC_NFE_AF|ExAC_SAS_AC|ExAC_SAS_AF|ExAC_nonTCGA_AC|ExAC_nonTCGA_AF|ExAC_nonTCGA_AFR_AC|ExAC_nonTCGA_AFR_AF|ExAC_nonTCGA_AMR_AC|ExAC_nonTCGA_AMR_AF|ExAC_nonTCGA_Adj_AC|ExAC_nonTCGA_Adj_AF|ExAC_nonTCGA_EAS_AC|ExAC_nonTCGA_EAS_AF|ExAC_nonTCGA_FIN_AC|ExAC_nonTCGA_FIN_AF|ExAC_nonTCGA_NFE_AC|ExAC_nonTCGA_NFE_AF|ExAC_nonTCGA_SAS_AC|ExAC_nonTCGA_SAS_AF|ExAC_nonpsych_AC|ExAC_nonpsych_AF|ExAC_nonpsych_AFR_AC|ExAC_nonpsych_AFR_AF|ExAC_nonpsych_AMR_AC|ExAC_nonpsych_AMR_AF|ExAC_nonpsych_Adj_AC|ExAC_nonpsych_Adj_AF|ExAC_nonpsych_EAS_AC|ExAC_nonpsych_EAS_AF|ExAC_nonpsych_FIN_AC|ExAC_nonpsych_FIN_AF|ExAC_nonpsych_NFE_AC|ExAC_nonpsych_NFE_AF|ExAC_nonpsych_SAS_AC|ExAC_nonpsych_SAS_AF|FATHMM_converted_rankscore|FATHMM_pred|FATHMM_score|GENCODE_basic|GERP++_NR|GERP++_RS|GERP++_RS_rankscore|GM12878_confidence_value|GM12878_fitCons_rankscore|GM12878_fitCons_score|GTEx_V8_gene|GTEx_V8_tissue|GenoCanyon_rankscore|GenoCanyon_score|Geuvadis_eQTL_target_gene|H1-hESC_confidence_value|H1-hESC_fitCons_rankscore|H1-hESC_fitCons_score|HGVSc_ANNOVAR|HGVSc_VEP|HGVSc_snpEff|HGVSp_ANNOVAR|HGVSp_VEP|HGVSp_snpEff|HUVEC_confidence_value|HUVEC_fitCons_rankscore|HUVEC_fitCons_score|Interpro_domain|LINSIGHT|LINSIGHT_rankscore|LIST-S2_pred|LIST-S2_rankscore|LIST-S2_score|LRT_Omega|LRT_converted_rankscore|LRT_pred|LRT_score|M-CAP_pred|M-CAP_rankscore|M-CAP_score|MPC_rankscore|MPC_score|MVP_rankscore|MVP_score|MetaLR_pred|MetaLR_rankscore|MetaLR_score|MetaRNN_pred|MetaRNN_rankscore|MetaRNN_score|MetaSVM_pred|MetaSVM_rankscore|MetaSVM_score|MutPred_AAchange|MutPred_Top5features|MutPred_protID|MutPred_rankscore|MutPred_score|MutationAssessor_pred|MutationAssessor_rankscore|MutationAssessor_score|MutationTaster_AAE|MutationTaster_converted_rankscore|MutationTaster_model|MutationTaster_pred|MutationTaster_score|PROVEAN_converted_rankscore|PROVEAN_pred|PROVEAN_score|Polyphen2_HDIV_pred|Polyphen2_HDIV_rankscore|Polyphen2_HDIV_score|Polyphen2_HVAR_pred|Polyphen2_HVAR_rankscore|Polyphen2_HVAR_score|PrimateAI_pred|PrimateAI_rankscore|PrimateAI_score|REVEL_rankscore|REVEL_score|Reliability_index|SIFT4G_converted_rankscore|SIFT4G_pred|SIFT4G_score|SIFT_converted_rankscore|SIFT_pred|SIFT_score|SiPhy_29way_logOdds|SiPhy_29way_logOdds_rankscore|SiPhy_29way_pi|TSL|TWINSUK_AC|TWINSUK_AF|UK10K_AC|UK10K_AF|Uniprot_acc|Uniprot_entry|VEP_canonical|VEST4_rankscore|VEST4_score|VindijiaNeandertal|aaalt|aapos|aaref|alt|bStatistic|bStatistic_converted_rankscore|cds_strand|chr|clinvar_MedGen_id|clinvar_OMIM_id|clinvar_Orphanet_id|clinvar_clnsig|clinvar_hgvs|clinvar_id|clinvar_review|clinvar_trait|clinvar_var_source|codon_degeneracy|codonpos|fathmm-MKL_co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pd3 commented 3 years ago

Thank you. The ambiguity of the AF tag is only a warning. What caused the error was the pos(1-based) part of the consequence definition. The commit 42baa31 works around this. Also it allows to get rid of the ambiguity (and thus the warning) by extending the -p option to work in this situation too. For example, if the field pos was in uppercase instead, this will work now:

bcftools +split-vep -f '%CSQ\n' -d -A tab input.vcf -p x
bcftools +split-vep -f '%POS %xPOS\n' input.vcf -p x
JannahS commented 3 years ago

Thank you for your quick reply. I'm now getting a new error

Error: no such tag defined in the VCF header: INFO/FunMotifs

Is there an option to just skip any undefined tag? such as using an option available for bcftools query ? -u, --allow-undef-tags do not throw an error if there are undefined tags in the format string, print "." instead

pd3 commented 3 years ago

The -u option has been now added.