Bacterial VCF file annotation using snpEff error

Question

[1769mkc]

These are the three bacterial data base i get hit from the snpEff database when I query which are these.

Genome  Organism
    Bacillus_pacificus_gca_001884025    Bacillus_pacificus_gca_001884025        
    Bacillus_pacificus_gca_003858675    Bacillus_pacificus_gca_003858675        
    Bacillus_pacificus_gca_006349595    Bacillus_pacificus_gca_006349595    

To test the above i tool out the output from the DRAGEN Small Whole Genome Sequencing

MiSeq i100: sWGS(5 GB) 

Project and downloaded the Bpacificus-ATCC10987-rep3-sWGS-MiSeqi100-241111.hard-filtered.vcf

file and filtered those which are only in the PASS category. I tried to annotate the filtered vcf file using SnpEff

snpEff Bacillus_pacificus_gca_003858675  Bpacificus-ATCC10987-rep3-sWGS-MiSeqi100-241111.hard-filtered.vcf > Bpacificus-ATCC10987_annot.vcf

I get something like this

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Bpacificus-ATCC10987-rep3-sWGS-MiSeqi100-241111
chr 293795  .   C   CA  .   PASS    DP=54;MQ=250.00;FractionInformativeReads=1.000;SoftClipRatio=0.01;ANN=CA||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND   GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB  1:66.12:0,54:1.0000:0,32:0,22:54:0,0,28,26:0,0,28,26
chr 394760  .   T   TG  .   PASS    DP=71;MQ=250.00;FractionInformativeReads=0.986;SoftClipRatio=0.03;ANN=TG||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND   GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB  1:66.42:0,70:1.0000:0,30:0,40:70:0,0,39,31:0,0,37,33
chr 399776  .   A   AT  .   PASS    DP=72;MQ=250.00;FractionInformativeReads=1.000;SoftClipRatio=0.00;ANN=AT||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND   GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB  1:66.44:0,72:1.0000:0,33:0,39:72:0,0,29,43:0,0,38,34
chr 630844  .   G   GT  .   PASS    DP=56;MQ=250.00;FractionInformativeReads=0.982;SoftClipRatio=0.00;ANN=GT||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND   GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB  1:66.14:0,55:1.0000:0,26:0,29:55:0,0,30,25:0,0,25,30

where I see the chromosome not found error. Even I tried in galaxy it the same result.

Any suggestion how do I match the chromosome name or it has some other issues in the vcf file which is causing the error.

[Pierre Lindenbaum]

in https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001884025.1/ and if you look at the files under the FTP tab, you'll see many different names for each contig: not just "chr"

#gtf-version 2.2
#!genome-build ASM188402v1
#!genome-build-accession NCBI_Assembly:GCF_001884025.1
#!annotation-date 04/11/2024 13:00:15
#!annotation-source NCBI RefSeq GCF_001884025.1-RS_2024_04_11
NZ_MACD01000002.1
NZ_MACD01000003.1
NZ_MACD01000004.1
NZ_MACD01000005.1
NZ_MACD01000006.1
NZ_MACD01000007.1
NZ_MACD01000008.1
NZ_MACD01000009.1
NZ_MACD01000010.1
NZ_MACD01000011.1
NZ_MACD01000012.1
NZ_MACD01000013.1
NZ_MACD01000014.1
NZ_MACD01000015.1
NZ_MACD01000016.1

[1769mkc]

okay I will explore this and update...

[Pierre Lindenbaum]

by the way, you could also look in the snpeff data directory where data are usually grouped on the name of the chromosomes.

[1769mkc]

Im yet to explore that I was trying to find from their site repository, but this I will check