[ensembl-dev] dev-owner at ensembl.org

Helen Schuilenburg helens at ebi.ac.uk
Thu Jun 13 09:05:37 BST 2019

Hi David

On 07/06/2019 18:44, David Tamborero wrote:
> Hi Helen
> FYI, if I m not wrong at this time of the day, VEP run (--tab output) 
> stops(w/o any msg or warning file created) as soon as a line 
> with REF==ALT is reached, so it does not seem to need to 'accumulate' 
> a number of these 'non-variant' entries
I am looking into this. Is the variant following the line with REF==ALT 
on the same chromosome?
> on the other hand, as you say, when using vcf as output with the 
> --allow_non_variant flag, entries as e.g.
> 12 111352091 16500 C C . PASS
> are included in the output w/o any annotation,
When using VCF format as input and output, by default VEP will skip 
non-variant lines of input (where the ALT allele is null).

Enabling the --allow_non_variant option the lines will be printed in the 
VCF output with no consequence data added.

VEP expects the ALT allele to be null to skip non-variant lines e.g.

22    17181903    var_1    A    G    .    .    .
22    17188416    var_2    T    .    .    .    .
22    19353405    var_3    G    A    .    .    .


> thanks!
> and have a nice weekedn
> d
> El vie., 7 jun. 2019 a las 18:25, Helen Schuilenburg 
> (<helens at ebi.ac.uk <mailto:helens at ebi.ac.uk>>) escribió:
>     Hi David
>     Thanks for the information.
>     The VEP should skip non-variant lines of input by default and not
>     stop.
>     We will look at updating the stats to report the lines skiped.
>     When using VCF format as input and output, by default VEP will
>     skip non-variant lines of input.  Please could you try running
>     your sample variants with vcf output (--vcf) and --allow_non_variant.
>     https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt
>     With the text output, it should also skip the non-variant lines.
>     VEP could be stopping on your input file, if it has skipped a
>     number of non-variant lines. We will look into this
>     Regards
>     Helen

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