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

[Stefan Gräf]

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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