VEP doesn't annotate spanning or overlapping deletions (* allele)

uab-cgds-worthey / DITTO

Variant Deleteriousness prediction tool using AI

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VEP doesn't annotate spanning or overlapping deletions (* allele) #4

Closed ManavalanG closed 1 year ago

ManavalanG commented 3 years ago

VEP appears to be silently ignoring spanning or overlapping deletion (* allele) variants during annotation. Note that in the screenshot below, spanning deletion variants do not have CSQ field in INFO column:

ManavalanG commented 3 years ago

Looked for VEP warning file (specified via --warning_file) for the corresponding samples, but these files were not present. VEP didn't create them.
Checked corresponding slurm job log file but no warnings/errors concerning this are present.

ManavalanG commented 3 years ago

Checked VEP's github issues and nothing relevant to this were found.
Note that spanning or overlapping deletions (* allele) are introduced in vcf spec v4.2.
Does VEP support vcf spec v4.2? VEP doesn't officially seem to say anything about this, but it is likely not supported. VCF spec v4.1 was released in 2013 and it wasn't supported by VEP until recently in 2020.
Fyi, their doc says this about vcf support:

VEP also supports using VCF (Variant Call Format) version 4.0.

tkmamidi commented 1 year ago

We're moving to a different annotation service since #16. So, closing the issue.