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

[Will McLaren]

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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