ALLELE_NUM undefined for some variants

[mskcc]

ALLELE_NUM undefined for some variants

[ewabergmann]

test variant:
5 67591092 . G GTAT

[ckandoth]

Unable to reproduce this by running vcf2maf on the test variant. The vep.vcf file generated by VEP appears to contain the ALLELE_NUM as 1. Going to put this on hold. Let me know what you find. Note that I used VEP v82.

[ckandoth]

In this issue, we found that VEP will not report ALLELE_NUM for variants with SVTYPE defined in the input VCF's INFO field. I'm going to assume this is what happened in your case too. Regardless, I have pushed a fix that should handle this situation gracefully. But the recommendation is to remove SVTYPE from your VCF if it is simply a small indel. VEP seems to limit the information it reports, based on the specs that SVTYPE is for larger structural variants. Closing this issue, but feel free to reopen if you find more information on this.

Thanks again for reporting!

[ewabergmann]

Thanks for spotting the problem and fixing it!
Indeed, the variant I reported had "SVTYPE=INS" in the INFO field (Pindel always adds SVTYPE).

[ckandoth]

@liangkaiye FYI. SVTYPE gets interpreted as a larger structural variant by VEP in downstream pipelines, and calculation of consequence on the protein sequence is skipped.