[ensembl-dev] 2 questions

Maher, Matthew Matthew_Maher at MEEI.HARVARD.EDU
Fri Aug 4 22:11:54 BST 2017

1.  Is this the correct forum for asking a question about VEP
functionality?  if not, what is?

2.  In VEP, with --vcf output in use, invoking --custom annotations
seems to result in the new/custom values being added as new positional
values within the CSQ/ANN structure - and that structure can have any #
of value sets (possibly zero? I'm not sure).  The result of this
placement seems to be the new/custom annotations being unnecessarily
repeated (since they apply to the position, not the specific transcript
annotations) and potentially missed completely (in the case of no CSQ
entries).  Is there an option (I can't find it) to cause the new/custom
annotation to appear as a new standalone KEY=[VALUE,VALUE,...] entry in
the INFO field (outside of the CSQ entry), with a VCF header entry
indicating "Number=A" (one value per alternate allele)?

Thank You All

very nice tool, VEP!

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