[ensembl-dev] Annotations for Insertion and Deletions

[Salih Tuna]

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_p
redictor.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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