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

[Stefan Gräf]

Hi Sarah,

Do you have an estimate when this might get resolved?

Many thanks,
 Stefan


On 2 December 2015 at 12:38, Sarah Hunt <seh at ebi.ac.uk> wrote:

>
> 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
> 15 40308859 . G T,A . PASS .
> #CUSTOM: ExAC.r0.3.vcf.gz
> 15 40308859 rs35602605 G T,A 2.40354e+07 PASS AC=15765,6
> =>VEP:
> 15 40308859 . G T,A . PASS ExAC_AC=15765,6;ExAC=rs35602605
>
> #INPUT: test.vcf
> 15 40308859 . G T,A . PASS .
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T,A . PASS ExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test.vcf
> 15 40308859 . G T,A . PASS .
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T,A . PASS ExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test.vcf
> 15 40308859 . G T,A . PASS .
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> =>VEP:
> 15 40308859 . G T,A . PASS ExAC.common_AC=15765;ExAC.common=.
>
>
> #INPUT: test_rev.vcf
> 15 40308859 . G A,T . PASS .
> #CUSTOM: ExAC.r0.3.vcf.gz
> 15 40308859 rs35602605 G T,A 2.40354e+07 PASS AC=15765,6
> =>VEP:
> 15 40308859 . G A,T . PASS ExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_rev.vcf
> 15 40308859 . G A,T . PASS .
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G A,T . PASS ExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_rev.vcf
> 15 40308859 . G A,T . PASS .
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G A,T . PASS ExAC.rare=.;ExAC.rare_AC=6
>
> #INPUT: test_rev.vcf
> 15 40308859 . G A,T . PASS .
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> =>VEP:
> 15 40308859 . G A,T . PASS ExAC.common=.;ExAC.common_AC=15765
>
>
> #INPUT: test_norm.vcf
> 15 40308859 . G T . PASS .
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.vcf.gz
> 15 40308859 rs35602605 G T,A 2.40354e+07 PASS AC=15765,6
> =>VEP:
> 15 40308859 . G T . PASS ExAC_AC=15765,6;ExAC=rs35602605
> 15 40308859 . G A . PASS ExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_norm.vcf
> 15 40308859 . G T . PASS .
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T . PASS ExAC.norm_AC=6;ExAC.norm=.
> 15 40308859 . G A . PASS ExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_norm.vcf
> 15 40308859 . G T . PASS .
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T . PASS ExAC.rare_AC=6;ExAC.rare=.
> 15 40308859 . G A . PASS ExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test_norm.vcf
> 15 40308859 . G T . PASS .
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> =>VEP:
> 15 40308859 . G T . PASS ExAC.common=.;ExAC.common_AC=15765
> 15 40308859 . G A . PASS ExAC.common=.;ExAC.common_AC=15765
>
>
> #INPUT: test_common.vcf
> 15 40308859 . G T . PASS .
> #CUSTOM: ExAC.r0.3.vcf.gz
> 15 40308859 rs35602605 G T,A 2.40354e+07 PASS AC=15765,6
> =>VEP:
> 15 40308859 . G T . PASS ExAC=rs35602605;ExAC_AC=15765,6
>
> #INPUT: test_common.vcf
> 15 40308859 . G T . PASS .
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T . PASS ExAC.norm_AC=6;ExAC.norm=.
>
> #INPUT: test_common.vcf
> 15 40308859 . G T . PASS .
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G T . PASS ExAC.rare=.;ExAC.rare_AC=6
>
> #INPUT: test_common.vcf
> 15 40308859 . G T . PASS .
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> =>VEP:
> 15 40308859 . G T . PASS ExAC.common_AC=15765;ExAC.common=.
>
>
> #INPUT: test_rare.vcf
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.vcf.gz
> 15 40308859 rs35602605 G T,A 2.40354e+07 PASS AC=15765,6
> =>VEP:
> 15 40308859 . G A . PASS ExAC_AC=15765,6;ExAC=rs35602605
>
> #INPUT: test_rare.vcf
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.norm.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G A . PASS ExAC.norm=.;ExAC.norm_AC=6
>
> #INPUT: test_rare.vcf
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.rare.vcf.gz
> 15 40308859 . G A 2.40354e+07 PASS AC=6
> =>VEP:
> 15 40308859 . G A . PASS ExAC.rare_AC=6;ExAC.rare=.
>
> #INPUT: test_rare.vcf
> 15 40308859 . G A . PASS .
> #CUSTOM: ExAC.r0.3.common.vcf.gz
> 15 40308859 . G T 2.40354e+07 PASS AC=15765
> =>VEP:
> 15 40308859 . G A . PASS ExAC.common=.;ExAC.common_AC=15765
>
>
>
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