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

Sarah Hunt seh at ebi.ac.uk
Mon Dec 7 14:10:26 GMT 2015 

Hi Stefan,

This will not be in release 83 when it comes out this week, but will be 
available in release 84, if not before.

Best wishes,

Sarah

On 04/12/2015 11:31, Stefan Gräf 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 
> <mailto: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
>>     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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>
>

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