[ensembl-dev] Annotations for Insertion and Deletions

Will McLaren wm2 at ebi.ac.uk
Wed Oct 19 13:59:19 BST 2011


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?



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_predictor.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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