[ensembl-dev] Is it a bug in ensembl_v79?

[Will McLaren]

Hello,

The error you report is a bug that was fixed a couple of days ago; if you
update your API code (either re-run INSTALL.pl or use "git pull" in the
ensembl-variation directory if you installed the API from GitHub) you
should no longer see this error.

The warning messages you see are because your input chromosome coordinates
are not valid for build GRCh38; note the difference in chromosome length
for chr22 between GRCh38:

http://www.ensembl.org/Homo_sapiens/Location/Chromosome?r=22

and GRCh37

http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=22

You should only use input files that have been called against or remapped
to GRCh38 when using the GRCh38 cache; the VEP does NOT do any remapping
for you. If you wish to remap your data from GRCh37 to GRCh38, you can try
the Assembly Converter tool - it comes as part of the ensembl-tools
package, or you can use it online here:
http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core

Regards

Will McLaren
Ensembl Variation

On 18 March 2015 at 07:32, namchul ghim <chulghim at gmail.com> wrote:

> After installing Ensembl_v79, I annotated vep cache with GRch37.
> When doing so I got a following message:
> Can't call method "impact" on an undefined value at
> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor
> /Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.
>
> When I checked the following source file, there is no definition of
> imapct() function. There is only function name in the same line.
> Isn't that a bug?
>
> Also, in same condition, annotating only vep cache with GRCh38 version was
> successful.
>
> What is going on?
>
> Additionally, when I was annotating vep cache with GRCh38 version, there
> is a warning message in cache file.
> The warning message is as follow:
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find cache for 22:51000001-52000000
> WARNING: Could not find cache for 22:51000001-52000000
>
> When I checked the actual cache folder, there is no file in such range. Is
> this something I should consider or can I ignore this message?
>
> For your information, the vep cahce is downloaded in this location:
>
> ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz
>
> Thank you very much!
>
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