[ensembl-dev] Annotations for Insertion and Deletions

[Salih Tuna]

Hi Will,
That makes lot of sense. Thanks. I just went through the output file and can
spot the output.
Thanks a lot.
Best,
Salih 


On 19/10/2011 14:15, "Will McLaren" <wm2 at ebi.ac.uk> wrote:

> 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      -       -       -       -       -       -
> 
> Cheers
> 
> Will
> 
> 
> 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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>>>> 
>> 
>> 
>> 
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