vcf file error
i am trying to annotate the vcf file through snpeff tool for the prokaryotic genome(i.e. Serratia marcescens ww4) but while annotating the error is coming as chromosome not found.
can someone give me the solution or some suggestions please.....
ERRORS: Some errors were detected Error type Number of errors ERROR_CHROMOSOME_NOT_FOUND 167917
the vcf file is also correct it is not a corrupted file i checked.
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Check if the reference genome you use has chromosome names matching the one used to generate the VCF file. Sometimes, different versions of the reference genome have different chromosome naming and this creates a problem.
thankyou for the suggestion i will look into that........ and let u know.