UGENE Forum - Error Variant annotation "chromosome not found"

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Error Variant annotation "chromosome not found" (Read 17056 times)

Mar 1^st, 2021 at 4:46pm

joseluis Offline
YaBB Newbies

Posts: 8

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

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Reply #1 - Mar 2^nd, 2021 at 1:03pm

Dmitrii Sukhomlinov Offline
YaBB Administrator
Russia

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Posts: 78

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.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

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Reply #2 - Mar 4^th, 2021 at 2:14pm

joseluis Offline
YaBB Newbies

Posts: 8

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.

variations.vcf (152 KB | 259 )

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