I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff, SnpSift.

    first pair vcf -> only variations| CASES and CONTROLS
    second pair vcf -> variations + SnpEff | CASES and CONTROLS
    third pair vcf-> variations + SnpEff+VEP+SnpSIFT| CASES and CONTROLS | at so on

Because it have non-overlapping samples, i tried to merge corresponding vcf of CASE and CONTROLS into one file with bcftools merge.

    bgzip -c file.vcf > file.vcf.gz
    tabix -p vcf file.vcf.gz
    bcftools merge -o merged.vcf.gz -Oz file.vcf.gz file_2.vcf.gz

Unfortunatelly  in files with SnpSift annotations i got this error:

    Error at chr1:20724637: wrong number of fields in dbNSFP_ada_score?

Please anybody knows how to solved this error or what does it mean?




your vcf is badly annotated.

there is a VCF with 6 ALT alleles : 

   chr1 20724637 rs1280663306;rs1445195248 TGGGAGGGAGGGAGAGAGGT TGGGAGGGAGAGAGGT,TGGGAGGGAGGGAGGGAGGT,TGGGAGGGAGGGAGAGAGGG,TGGGGGGGAGGGAGAGAGGT,TGGGTGGGAGGGAGAGAGGT,TGGGAGAGAGGGAGAGAGGT 


and the annotation for dbNSFP_ada_score is `INFO=<ID=dbNSFP_ada_score,Number=A,Ty..`:

so `Number=A` implies that there MUST be one value for each ALT allele.

but there is only 3 values for this variant: `0.016,0.054,0.0` while there is 6 ALT alleles.

