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

Fri Dec 4 22:09:27 GMT 2015

Hi Stefan,

If you're using the --custom option only for ExAC, have you looked into
using the related VEP plugin
<https://github.com/Ensembl/VEP_plugins/blob/master/ExAC.pm>? This link
describes how to set up VEP with the ExAC plugin:
https://github.com/mskcc/vcf2maf#install-vep

You'd call VEP with the following argument to report AC, AN, and AF. It
won't fetch rsIDs from the ExAC VCF, but VEP can report that anyway.

--plugin ExAC,/path/to/ExAC/ExAC.r0.3.sites.vep.vcf.gz,AC,AN

Cheers!

~Cyriac

On Fri, Dec 4, 2015 at 6:31 AM, Stefan Gräf <sg550 at cam.ac.uk> wrote:

> 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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>
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