[ensembl-dev] VEP (v82) custom annotation returned with wrong information

Sarah Hunt seh at ebi.ac.uk
Wed Dec 2 12:38:17 GMT 2015


Hi Stefan,

You are correct - custom annotation uses only position information to 
extract features. Thanks for pointing out this causes problems when 
variants with 2 alternate alleles are split over two lines in the VCF - 
we will look at taking allele information into account.

All the best,

Sarah

On 01/12/2015 18:26, Stefan Gräf wrote:
>
> Hi Will et al.,
>
> We have come across an issue when annotating with the --custom option. 
> It seems that the alternative allele is not taken into account for the 
> annotation and therefore the wrong information is associated with the 
> respective allele in almost all cases. I have attached some test data 
> and a test script (test.sh) that runs through all the combinations for 
> sites with 1 and 2 alternative alleles. The annotated transcript of 
> the script can be seen below (correct annotation highlighted in green, 
> faulty annotation in red). A quick fix would be very much appreciated.
>
> All best,
>  Stefan
>
>
> $ . ./test.sh
>
> #INPUT: test.vcf
> 1540308859.GT,A.PASS.
> #CUSTOM: ExAC.r0.3.vcf.gz
> 1540308859rs35602605GT,A2.40354e+07PASSAC=15765,6
> =>VEP:
> 1540308859.GT,A.PASSExAC_AC=15765,6;ExAC=rs35602605
>
> #INPUT: test.vcf
> 1540308859.GT,A.PASS.
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT,A.PASSExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test.vcf
> 1540308859.GT,A.PASS.
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT,A.PASSExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test.vcf
> 1540308859.GT,A.PASS.
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> =>VEP:
> 1540308859.GT,A.PASSExAC.common_AC=15765;ExAC.common=.
>
>
> #INPUT: test_rev.vcf
> 1540308859.GA,T.PASS.
> #CUSTOM: ExAC.r0.3.vcf.gz
> 1540308859rs35602605GT,A2.40354e+07PASSAC=15765,6
> =>VEP:
> 1540308859.GA,T.PASSExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_rev.vcf
> 1540308859.GA,T.PASS.
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GA,T.PASSExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_rev.vcf
> 1540308859.GA,T.PASS.
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GA,T.PASSExAC.rare=.;ExAC.rare_AC=6
>
> #INPUT: test_rev.vcf
> 1540308859.GA,T.PASS.
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> =>VEP:
> 1540308859.GA,T.PASSExAC.common=.;ExAC.common_AC=15765
>
>
> #INPUT: test_norm.vcf
> 1540308859.GT.PASS.
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.vcf.gz
> 1540308859rs35602605GT,A2.40354e+07PASSAC=15765,6
> =>VEP:
> 1540308859.GT.PASSExAC_AC=15765,6;ExAC=rs35602605
> 1540308859.GA.PASSExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_norm.vcf
> 1540308859.GT.PASS.
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT.PASSExAC.norm_AC=6;ExAC.norm=.
> 1540308859.GA.PASSExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_norm.vcf
> 1540308859.GT.PASS.
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT.PASSExAC.rare_AC=6;ExAC.rare=.
> 1540308859.GA.PASSExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test_norm.vcf
> 1540308859.GT.PASS.
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> =>VEP:
> 1540308859.GT.PASSExAC.common=.;ExAC.common_AC=15765
> 1540308859.GA.PASSExAC.common=.;ExAC.common_AC=15765
>
>
> #INPUT: test_common.vcf
> 1540308859.GT.PASS.
> #CUSTOM: ExAC.r0.3.vcf.gz
> 1540308859rs35602605GT,A2.40354e+07PASSAC=15765,6
> =>VEP:
> 1540308859.GT.PASSExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_common.vcf
> 1540308859.GT.PASS.
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT.PASSExAC.norm_AC=6;ExAC.norm=.
>
> #INPUT: test_common.vcf
> 1540308859.GT.PASS.
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GT.PASSExAC.rare=.;ExAC.rare_AC=6
>
> #INPUT: test_common.vcf
> 1540308859.GT.PASS.
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> =>VEP:
> 1540308859.GT.PASSExAC.common_AC=15765;ExAC.common=.
>
>
> #INPUT: test_rare.vcf
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.vcf.gz
> 1540308859rs35602605GT,A2.40354e+07PASSAC=15765,6
> =>VEP:
> 1540308859.GA.PASSExAC_AC=15765,6;ExAC=rs35602605
>
> #INPUT: test_rare.vcf
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GA.PASSExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_rare.vcf
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 1540308859.GA2.40354e+07PASSAC=6
> =>VEP:
> 1540308859.GA.PASSExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test_rare.vcf
> 1540308859.GA.PASS.
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 1540308859.GT2.40354e+07PASSAC=15765
> =>VEP:
> 1540308859.GA.PASSExAC.common=.;ExAC.common_AC=15765
>
>
>
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