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

Anja Thormann anja at ebi.ac.uk
Wed Feb 28 09:27:35 GMT 2018


Hi Matthew,

could you please provide a few more details? We need to know the ensembl-vep version and the exact command line you are using. That should make it easier for us to find the cause of the problem.

Thank you
Anja

> On 27 Feb 2018, at 19:55, Maher, Matthew <Matthew_Maher at MEEI.HARVARD.EDU> wrote:
> 
> 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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