[ensembl-dev] VEP variants missing on output

[Guillermo Marco Puche]

Hello,

I've been checking VEP results, and i've noticed that I'm missing some 
input variants in the output.

I think this may be issued to some of the options i'm using to launch vep:

hgvs               1
canonical          1
ccds               1
check_svs          1
domains            1
gmaf               1
hgnc               1
maf_1kg            1
numbers            1
polyphen           b
regulatory         1
sift               b

Should be any of these options filtering output? I've disabled all 
plugins to run this test to be sure that it's not a plugin issue.

  * With a 406 variant input vcf file, I've missed 16 variants.
  * I then ran VEP with only those 16 missing variants and missed 3 on
    output.
  * Rerun again and now with 3 missing variants and now not a single one
    was missing.

I would like to know what's behind that weird behaviour.

Thank you.

Best regards,
Guillermo.



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