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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Error Variant annotation "chromosome not found" https://forum.ugene.net/forum/YaBB.pl?num=1614591972 Message started by joseluis on Mar 1^st, 2021 at 4:46pm

Title: Error Variant annotation "chromosome not found"
Post by joseluis on Mar 1^st, 2021 at 4:46pm

Hello. When I try to annotate variants from a a vcf file I recieve the following error message. How can I solve it?

ERROR_CHROMOSOME_NOT_FOUND: Chromosome does not exists in reference genome database. Typically indicates a mismatch between the chromosome names in the input file and the chromosome names used in the reference genome. (count: 960)

Thank you

Title: Re: Error Variant annotation "chromosome not found"
Post by Dmitrii Sukhomlinov on Mar 2^nd, 2021 at 1:03pm

Hello,

This problem has several reasons to appear, so it's difficult to figure it out without the input data. Could you, please, provide your .vcf file and which genome do you use?

As far as I understand, you try to run the "Variation annotation with SnpEff" workflow? If not, please, describe the way you have this error.

Title: Re: Error Variant annotation "chromosome not found"
Post by joseluis on Mar 4^th, 2021 at 2:14pm

Hello. First I use "Variant calling" tool -> Reference Sequence file: GRCh38. I get the attached vcf.file. Then I use "Variation annotation with SnpEff" tool -> input file: vcf.file and genome: hg38.
Thank you.

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=variations.vcf (152 KB | 235 )