[ensembl-dev] VEP question (--hgvs option)

Maher, Matthew Matthew_Maher at MEEI.HARVARD.EDU
Tue Feb 27 19:55:46 GMT 2018


Hi-

I am using VEP and hoping to the appropriate HGVS nomenclature and so
have turned on the --hgvs options.  On first attempt, I saw all Ns in
the output for the reference bases.   Reading the docs and FAQs, I saw
that I needed to also be sure to supply the reference sequence via the
--fasta option.  I did that, and VEP seems to recognize this, as it does
auto-index the file the first time.  And now I do see some of the
reference bases being filled in on the HGVS output - but only some -
many of the results still contain 'N'. Seems sort random which ones have
Ns and which have base.   And rerunning the same input file, I was
noticing that the very same variant that had correct base on one run,
would get the 'N' on the next run (or vice versa).  This sort of
non-determinism in the output makes me think that sort of
threading/forking behavior is behind the variation.  I am using the
--forks option (with either 4 or 8) to speed things up.

What do you think could be the reason for the inconsistent filling of
reference bases on the HGVS output?

--forks?

If not, can you recommend steps to diagnose the issue?

Thanks

Matthew Maher
Massachusetts Eye and Ear Infirmary


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