Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
Error Variant annotation "chromosome not found" (Read 662 times)
Mar 1st, 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
 
IP Logged
 
Reply #1 - Mar 2nd, 2021 at 1:03pm

Dmitrii Sukhomlinov   Offline
YaBB Administrator
Russia

Gender: male
Posts: 54
*****
 
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,
UGENE team.
IP Logged
 
Reply #2 - Mar 4th, 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 | 48 )
IP Logged
 
Page Index Toggle Pages: 1