[ensembl-dev] dev-owner at ensembl.org
david.tamborero at gmail.com
Tue Jun 18 10:08:42 BST 2019
(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 '.' ?
El jue., 13 jun. 2019 a las 10:06, Helen Schuilenburg (<helens at ebi.ac.uk>)
> 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.
> #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 . . .
> and have a nice weekedn
> El vie., 7 jun. 2019 a las 18:25, Helen Schuilenburg (<helens at ebi.ac.uk>)
>> 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.
>> 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
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