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

[David Tamborero]

Hi Helen,

(sorry for the late response, i was travelling)

indeed, it looks like the combo to make the VEP run stop is:

- --tab as output format
- the REF==ALT
- the next line to the REF==ALT entry is *a different* chromosome

on the other hand, regarding the 'concept' of null variant, do you think
that a REF==ALT should be considered as so? I mean, should not be annotated
as silent, as opposite to true 'non valid' variant statements as that
passing an ALT of '.' ?

thanks!
d

El jue., 13 jun. 2019 a las 10:06, Helen Schuilenburg (<helens at ebi.ac.uk>)
escribió:

> 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.
>
>
> ##fileformat=VCFv4.0
> #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
> 22    17181903    var_1    A    G    .    .    .
> 22    17188416    var_2    T    .    .    .    .
> 22    19353405    var_3    G    A    .    .    .
>
> Regards
> Helen
>
>
> thanks!
> and have a nice weekedn
> d
>
>
> El vie., 7 jun. 2019 a las 18:25, Helen Schuilenburg (<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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