Hi,

I annotated variants in a bacterial genome using snpEff, but when I saw snpEff_summary.html, there were 944 warnings colored in yellow. Varians were detected using gatk HaplotypeCaller.

When I saw the warnings, they were almost WARNING_TRANSCRIPT_NO_START_CODON. However, when I checked both reference genome and CDS, both have start codon.

I have no idea why they were tagged as warnings.

If anyone has any idea, that would help me a lot.

Thank you.

I annotated using this command

 java -jar snpEff.jar -c snpEff.config -i vcf -o vcf bacteria1 SNPs_counted_using_HaplotypeCaller.vcf 1> res.vcf

one of the results I got

bacteria1   99501   .   C   A   697.6   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.555;DP=187;ExcessHet=3.0103;FS=0.784;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=3.73;ReadPosRankSum=0.989;SOR=0.762;ANN=A|upstream_gene_variant|MODIFIER|D9_0073|GENE_D9_0073|transcript|TRANSCRIPT_D9_0073|protein_coding||c.-4774G>T|||||4774|,A|upstream_gene_variant|MODIFIER|D9_0074|GENE_D9_0074|transcript|TRANSCRIPT_D9_0074|protein_coding||c.-4536G>T|||||4536|,A|upstream_gene_variant|MODIFIER|D9_0078|GENE_D9_0078|transcript|TRANSCRIPT_D9_0078|protein_coding||c.-768G>T|||||768|,A|upstream_gene_variant|MODIFIER|D9_0079|null|transcript|D9_0079|protein_coding||c.-698C>A|||||609|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|D9_0080|GENE_D9_0080|transcript|TRANSCRIPT_D9_0080|protein_coding||c.-2444C>A|||||2444|,A|upstream_gene_variant|MODIFIER|D9_0081|GENE_D9_0081|transcript|TRANSCRIPT_D9_0081|protein_coding||c.-3194C>A|||||3194|,A|upstream_gene_variant|MODIFIER|D9_0082|GENE_D9_0082|transcript|TRANSCRIPT_D9_0082|protein_coding||c.-4759C>A|||||4759|,A|downstream_gene_variant|MODIFIER|D9_0075|GENE_D9_0075|transcript|TRANSCRIPT_D9_0075|protein_coding||c.*3987C>A|||||3987|,A|downstream_gene_variant|MODIFIER|D9_0076|GENE_D9_0076|transcript|TRANSCRIPT_D9_0076|protein_coding||c.*3083C>A|||||3083|,A|downstream_gene_variant|MODIFIER|D9_0077|GENE_D9_0077|transcript|TRANSCRIPT_D9_0077|protein_coding||c.*2167C>A|||||2167|,A|intergenic_region|MODIFIER|D9_0078-D9_0079|GENE_D9_0078-null|intergenic_region|GENE_D9_0078-null|||n.99501C>A||||||  GT:AD:DP:GQ:PL  0/1:157,30:187:99:705,0,5786

I created my gtf file like this

seqname     source   feature start end   score strand frame attribute
bacteria1   bacteria1   CDS 101     1507    .   +   0   gene id "D9_0001";
bacteria1   bacteria1   CDS 1569    2666    .   +   0   gene id "D9_0002";
bacteria1   bacteria1   CDS 2663    4378    .   +   0   gene id "D9_0003";

I created my own database and adding this to snpEff.config

bacteria1.genome :bacteria1
bacteria1.chromosomes : bacteria1
bacteria1.bacteria1.codonTable : Bacterial_and_Plant_Plastid