[ensembl-dev] dev-owner at ensembl.org
Helen Schuilenburg
helens at ebi.ac.uk
Tue Jun 18 11:52:17 BST 2019
Hi David
On 18/06/2019 10:08, David Tamborero wrote:
> 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
>
There was a bug when the last entry on a chromosome was a variant with
REF==ALT.
We pushed a fix yesterday to our current release (release/96) and it
will be in future releases.
Thank you for reporting the problem.
> 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 '.' ?
>
When using the --allow_non_variant VEP expects a non-variant to be
represented with an ALT with the missing value (.)
If the variant has REF==ALT, the variant is not included in tab output
but included in VCF (with no consequence).
For vcf variants with REF==ALT, vcf-validator warns "REF allele listed
in the ALT field??"
We will review the REF==ALT in VEP and VEP documentation.
Regards
Helen
> thanks!
> d
>
> El jue., 13 jun. 2019 a las 10:06, Helen Schuilenburg
> (<helens at ebi.ac.uk <mailto: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 <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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