[ensembl-dev] VEP does not annotate all rows in a samtools VCF

[Marlies Dolezal]

hi Will,
thanks for your quick reply!
unfortunately using the  --allow_non_variant option gave the exact same
output.


-offline --allow_non_variant --force_overwrite --species bos_taurus --fork
16 - --input_file Chr$i.vcf --o Chr$i.vep

Start time 2014-04-28 10:27:05
End time 2014-04-28 10:36:57
Run time 592 seconds


Lines of input read 900857
Variants processed 900241
Variants remaining after filtering 900241


any other ideas?
thanks again!
regards, marlies


2014-04-28 10:24 GMT+02:00 Will McLaren <wm2 at ebi.ac.uk>:
>
> Hello,
>
> It's possible you have some non-variant lines in your VCF; these will
have a "." as the ALT allele column, something like:
>
> 21      26960070        .     G       .       .       .       .
>
> By default the VEP ignores these. You can force the VEP to allow them
through (though they still won't be annotated) using --allow_non_variant.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 28 April 2014 08:52, Marlies Dolezal <marlies.dolezal at gmail.com> wrote:
>>
>> hi all,
>>
>> i am using the latest VEP version 75 (API)(75) to annotate samtools VCF
files.
>>
>> -offline --force_overwrite --species bos_taurus --fork 16 --input_file
Chr$i.vcf --o Chr$i.vep
>>
>>
>> the General statistics section of the VEP_summary.html tells me that all
lines of my vcfs are read in, but only a subset of these are processed.
>> eg:
>> Lines of input read 900857
>> Variants processed 900241
>>
>> the difference in lines does not correspond to header/comment lines only.
>>
>> where can i find out which variants are not processed to try to figure
out why they are not processed?
>>
>> thanks a lot in advance
>> regards Marlies
>>
>>
>>
>>
>>
>>
>> --
>> Dr. Marlies Dolezal
>> 1030 Vienna
>> Austria/Europe
>>
>> marlies.dolezal(at)gmail.com
>>
>> “The great tragedy of science is the slaying of a beautiful hypothesis
by an ugly fact.”
>> Thomas Henry Huxley
>> (1825-1895)
>>
>>
>>
>>
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>
>
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--
Dr. Marlies Dolezal
1030 Vienna
Austria/Europe

marlies.dolezal(at)gmail.com

“The great tragedy of science is the slaying of a beautiful hypothesis by
an ugly fact.”
Thomas Henry Huxley
(1825-1895)
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