vcf2db does not create genotypes table

[ramashka328]

Hello Brent,

I am trying to run the vcf2db to create tables that will later be used by gemini. However, I do not get the table called genotypes. Except from this, it works as it should. Maybe you have an idea of what information is lacking here to create this table?

The vcf header (without contig info fields) before calling vcfanno looks like this:

##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference.">
##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">
##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call.">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block.">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##VEP="v107" time="2023-01-20 21:36:54" cache="/vep_data/homo_sapiens_merged/107_GRCh38" ensembl-variation=107.efb23bc ensembl=107.5f39899 ensembl-funcgen=107.0fbd7d5 ensembl-io=107.a473894 1000genomes="phase3" COSMIC="95" ClinVar="202201" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 41" genebuild="2014-07" gnomADe="r2.1.1" gnomADg="v3.1.2" polyphen="2.2.2" refseq="109.20211119 - GCF_000001405.39_GRCh38.p13_genomic.gff" regbuild="1.0" sift="sift5.2.2"
##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|HGVSg|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_NFE_AF|gnomADe_OTH_AF|gnomADe_SAS_AF|gnomADg_AF|gnomADg_AFR_AF|gnomADg_AMI_AF|gnomADg_AMR_AF|gnomADg_ASJ_AF|gnomADg_EAS_AF|gnomADg_FIN_AF|gnomADg_MID_AF|gnomADg_NFE_AF|gnomADg_OTH_AF|gnomADg_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|SpliceAI_cutoff|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|LoF|LoF_filter|LoF_flags|LoF_info|CADD_PHRED|CADD_RAW|REVEL">
##SpliceAI_cutoff=Flag if delta score pass the cutoff (PASS) or if it does not (FAIL)
##SpliceAI_pred_DP_AG=SpliceAI predicted effect on splicing. Delta position for acceptor gain
##SpliceAI_pred_DP_AL=SpliceAI predicted effect on splicing. Delta position for acceptor loss
##SpliceAI_pred_DP_DG=SpliceAI predicted effect on splicing. Delta position for donor gain
##SpliceAI_pred_DP_DL=SpliceAI predicted effect on splicing. Delta position for donor loss
##SpliceAI_pred_DS_AG=SpliceAI predicted effect on splicing. Delta score for acceptor gain
##SpliceAI_pred_DS_AL=SpliceAI predicted effect on splicing. Delta score for acceptor loss
##SpliceAI_pred_DS_DG=SpliceAI predicted effect on splicing. Delta score for donor gain
##SpliceAI_pred_DS_DL=SpliceAI predicted effect on splicing. Delta score for donor loss
##SpliceAI_pred_SYMBOL=SpliceAI gene symbol
##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)
##LoF_filter=Reason for LoF not being HC
##LoF_flags=Possible warning flags for LoF
##LoF_info=Info used for LoF annotation
##CADD_PHRED=PHRED-like scaled CADD score
##CADD_RAW=Raw CADD score
##REVEL=Rare Exome Variant Ensemble Learner

[brentp]

how did you run vcf2db.py ? can you show the command and the output (stderr, stdout)? did you send a pedigree file? can you show 1 row of the file (not the header)?