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

[Heidi Viitaniemi]

Hi Will,

And thank you for your response. I'll wait for the solution. I like the 
idea that you can incorporate your own data to run VEP.

Thanks,
Heidi Viitaniemi



19.3.2013 13:42, Will McLaren kirjoitti:
> 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 
> <mailto: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
>     <http://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 <http://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
>     <http://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
>     <http://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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-- 
______________________________________________

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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