[ensembl-dev] Annotations for Insertion and Deletions

[Salih Tuna]

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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