[ensembl-dev] Codon called wrong in VEP when using custom build cache

[Will McLaren]

Hello Heidi,

Thanks for finding this - the causes of this bug are I believe somewhat
complex so may take a while to get to the bottom of it.

Just wanted to let you know that your mail is not being ignored!

Regards

Will McLaren
Ensembl Variation


On 18 March 2013 13:48, Heidi Viitaniemi <hmviit at utu.fi> wrote:

>  Hi,
>
> I'm running version 2.7 on a unix server. I want to create a custom cache
> using my own gtf and fasta with gtf2vep.pl. This works without problem
> and also running VEP seems to go fine. The problem is that, in the output
> it seems that the cDNA_position, CDS_position and Protein_position are
> correct given my input gtf file but the calls for Amino_acids and Codons
> seem completely random. If I run against the cache retrieved from ensembl
> these are all correct. The version of the genome didn't have an effect on
> the output, the gtf's haven't changed. The gtf and the fasta that I'm using
> for the custom originate from the ensembl reference so I don't see any
> reason why the custom cache shouldn't perform the same way as the reference
> from ensembl cache. Could there be bug that somehow messes up the link
> between the custom gtf and fasta in my run? Below are the commands I ran
> and a snippet of the output's I got.
>
> Thanks,
> Heidi Viitaniemi
>
> For custom cache I'm running (wrong output for Amino_acids and Codons)
> perl gtf2vep.pl -i GasAcu1.67_group_xixflip.gtf -f
> gasAcu_group_withoutbac_inv7.fa -d 67 -s
> Gasterosteus_aculeatus_XIXflipped_18032013
> perl variant_effect_predictor.pl -offline 1 -dir $HOME/.vep -i
> ens_realigned_AK_F.var.vcf -format vcf -fork 4 -db_version 67 -species
> Gasterosteus_aculeatus_XIXflipped_18032013 -numbers -per_gene -buffer_size
> 10000 -o VEP_18032013_exon_pergene_AK_F.var.vcf.txt
>
>        groupXIX_2822477_C/T groupXIX:2822477 T ENSGACG00000003129
> ENSGACT00000004109 Transcript missense_variant 67 49 17 G/R Gga/Aga -
> EXON=1/2  groupXIX_2822500_T/C groupXIX:2822500 C ENSGACG00000003129
> ENSGACT00000004109 Transcript missense_variant 44 26 9 Y/C tAt/tGt -
> EXON=1/2  groupXIX_2822523_C/T groupXIX:2822523 T ENSGACG00000003129
> ENSGACT00000004109 Transcript synonymous_variant 21 3 1 R cgG/cgA -
> EXON=1/2  groupXIX_2822541_T/A groupXIX:2822541 A ENSGACG00000003129
> ENSGACT00000004109 Transcript 5_prime_UTR_variant 3 - - - - - EXON=1/2
>
> For ensembl cache I'm running (correct output for Amino_acids and Codons)
> perl variant_effect_predictor.pl -offline -dir $HOME/.vep -i
> ens_realigned_AK_F.var.vcf -format vcf -fork 4 -db_version 69 -species
> gasterosteus_aculeatus -numbers -per_gene -buffer_size 10000 -o
> ensVEP_18032013_exon_pergene_AK_F.var.vcf.txt
>
>        groupXIX_2822477_C/T groupXIX:2822477 T ENSGACG00000003129
> ENSGACT00000004109 Transcript missense_variant 67 49 17 A/T Gcg/Acg -
> EXON=1/2  groupXIX_2822500_T/C groupXIX:2822500 C ENSGACG00000003129
> ENSGACT00000004109 Transcript missense_variant 44 26 9 D/G gAc/gGc -
> EXON=1/2  groupXIX_2822523_C/T groupXIX:2822523 T ENSGACG00000003129
> ENSGACT00000004109 Transcript initiator_codon_variant 21 3 1 M/I atG/atA -
> EXON=1/2  groupXIX_2822541_T/A groupXIX:2822541 A ENSGACG00000003129
> ENSGACT00000004109 Transcript 5_prime_UTR_variant 3 - - - - - EXON=1/2
>
> --
> ______________________________________________
>
> Heidi Viitaniemi
> PhD student
> Division of Genetics and Physiology
> Department of Biology
> Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
> University of Turku
> 20520 Turku
>
> FINLAND
>
>
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