Comments (3)
ckandoth
commented on June 30, 2024
Thanks for reporting this. Let me take a look.
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ckandoth
commented on June 30, 2024
Sorry for putting this on the backburner. I tracked this down to a bug in VEP where it fails to report the Allele in the CSQ output, when you have SVTYPE=DEL specified in your INFO field. If you remove SVTYPE=DEL, it seems to work fine. Can you test this out and let me know? If you can confirm, then we'll report this to dev@ensembl.
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ckandoth
commented on June 30, 2024
Actually, it looks like more like a feature of VEP to annotate larger SVs (structural variants) differently. Allele is reported in CSQ, but it simply says deletion. It also skips reporting an HGVS notation of the variant and the exon/intron numbers. I have pushed a fixed vcf2maf.pl in the master branch that should handle this condition gracefully, but I'd recommend not defining SVTYPE in the INFO field, for small indels, so that VEP provides you with more granular information on them.
Thanks again for reporting this!
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Related Issues (20)
- Empty 't_depth' 't_ref_count' 't_alt_count' HOT 1
- Add options for RefSeq and Merged caches when converting to MAF
- ERROR: Failed to run the VEP annotator! HOT 2
- Running error HOT 3
- Why is empty in all database? HOT 1
- Option --retain-fmt doesn't work
- ERROR: Provided --ref-fasta is missing or empty HOT 3
- Update vcf2maf to work with later Ensembl vep releases HOT 2
- Release new tag HOT 4
- ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID
- ERROR: Failed to run the VEP annotator!
- The best solution for one-to-one correspondence between genes and transcripts HOT 3
- VCF2MAF and allele frequency HOT 4
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- HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108 HOT 3
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- Unrecognized biotype/effect HOT 2
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