[ensembl-dev] Annotations for Insertion and Deletions

Will McLaren wm2 at ebi.ac.uk
Wed Oct 19 14:15:56 BST 2011

Hi Salih,

The reason you don't see any results is because you are looking for
results for the position 143767179.

VCF defines insertions and deletions (and also any unbalanced
substitution) differently to how we do in Ensembl - VCF always include
the base before the actual variation in the alleles, and the position
of the variant refers to this base.

When we process the variant in the VEP, we have to convert it to
Ensembl world, where we don't include the base before. Hence, in your
example, T / TCATAA at position 143767179 becomes - / CATAA at
position 143767180.

You can avoid any confusion by giving the variants unique identifiers
in the third column of your VCF; this will appear as the first column
in the VEP output. This could be something as simple as combining the
chromosome and position.

Just to confirm, this is the output I see when I run your input:

#Uploaded_variation     Location        Allele  Gene    Feature
Feature_type    Consequence     cDNA_position
CDS_positionProtein_position Amino_acids     Codons
Existing_variation      Extra
1_143767180_-/CATAA     1:143767179-143767180   CATAA
ENSG00000236334 ENST00000419275 Transcript      3PRIME_UTR
702-703      -       -       -       -       -       -



On 19 October 2011 14:02, Salih Tuna <st5 at sanger.ac.uk> wrote:
> Hi Will,
> Here is the input from the vcf file
> chr1    143767179       .       T       TCATAA          0       CLUSTER
> AF=0.0375,DP=1.0,QF=2   GT:DP:AC        ./.:DP=0:AC=0.00
> ./.:DP=7:AC=0.67        ./.:DP=0:AC=0.00        ./.:DP=6:AC=1.00
>        ./.:DP=4:AC=0.00        ./.:DP=4:AC=1.00        ./.:DP=0:AC=0.00
> ./.:DP=1:AC=0.00        ./.:DP=0:AC=0.00        ./.:DP=1:AC=0.68
> ./.:DP=4:AC=0.00        ./.:DP=0:AC=0.67
> Thanks,
> Salih
> On 19/10/2011 13:59, "Will McLaren" <wm2 at ebi.ac.uk> wrote:
>> Hello,
>> Can you provide an example of the input you are using - I know you
>> have specified the position, but could you give me the actual line
>> from the VCF?
>> Cheers
>> Will
>> On 19 October 2011 13:02, Salih Tuna <st5 at sanger.ac.uk> wrote:
>>> Hi,
>>> I am using  emsembl API variant effect predictor (version 2.2) to annotate
>>> gene names,variations etc from the VCF file.
>>> I use the following command
>>> perl
>>> /nfs/users/nfs_s/st5/src/ensembl-variation/scripts/examples/variant_effect_pr
>>> edictor.pl
>>> -i syzygy_noannotation.vcf -o syzygy_annotation.vcf --check_existing
>>> The annotations works fine except when there is insertion or deletions.
>>> For example chr1:143767179 has insertion and is not annotated. There are
>>> many positions similar to this.
>>> I was wondering if you could help me with this problem?
>>> Thanks,
>>> Salih
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