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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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Annotation fails if contigs has no annotations in gtf #1798

Closed fperezcobos closed 1 week ago

fperezcobos commented 1 week ago

Describe the issue

I'm annotating a vcf coming from Manta with structural variants. I noticed that some variants are skipped with the following message:

WARNING: line 41 skipped (Un00432 41413 Un00432_41413_A_A]Un00047:89539]...): Chromosome Un00432 not found in annotation sources or synonyms; chromosome Un00432 does not overlap any features

I checked the fasta and gtf files and the contigs exist with the same exact name as in the warning message but none of them have annotations in the gft.

Additional information

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System

Full VEP command line

./vep -i formatted_SRX338100_SRR955759_vs_SRX2581517_SRR5277628_processed.vcf --gtf gtf_file.gz --fasta ntab.fa -o test_vep_annotation.txt --stats_file test_vep_annotation.stats.html --tab --fork 10 --buffer_size 500 --pick --minimal --dont_skip --force_overwrite

Full error message

WARNING: line 41 skipped (Un00432 41413 Un00432_41413_A_A]Un00047:89539]...): Chromosome Un00432 not found in annotation sources or synonyms; chromosome Un00432 does not overlap any features WARNING: line 42 skipped (Un00432 41498 Un00432_41498_G_G[Un00396:43504[...): Chromosome Un00432 not found in annotation sources or synonyms; chromosome Un00432 does not overlap any features WARNING: line 43 skipped (Un00523 424 Un00523_424T]Un00045:294530]T T ...): Chromosome Un00523 not found in annotation sources or synonyms; chromosome Un00523 does not overlap any features WARNING: line 44 skipped (Un00597 4502 Un00597_4502G[Un00597:8590[G G ...): Chromosome Un00597 not found in annotation sources or synonyms; chromosome Un00597 does not overlap any features WARNING: line 45 skipped (Un00597 8590 Un00597_8590A[Un00597:4502[A A ...): Chromosome Un00597 not found in annotation sources or synonyms; chromosome Un00597 does not overlap any features WARNING: line 46 skipped (Un00660 403 Un00660_403C]Un00662:2809]C C ]U...): Chromosome Un00660 not found in annotation sources or synonyms; chromosome Un00660 does not overlap any features WARNING: line 47 skipped (Un00662 2809 Un00662_2809_G_G[Un00660:403[ G G...): Chromosome Un00662 not found in annotation sources or synonyms; chromosome Un00662 does not overlap any features WARNING: line 48 skipped (Un00668 2421 Un00668_2421_T_T]Chr18:127887142]...): Chromosome Un00668 not found in annotation sources or synonyms; chromosome Un00668 does not overlap any features