[ensembl-dev] allele-specific annotation against a custom VCF
Katherine Smith
katherine.smith at genomicsengland.co.uk
Thu May 14 19:45:01 BST 2015
Dear ENSEMBL developers,
Is there any way to make VEP custom annotation against a VCF file allele-specific?
The custom annotation help page says "Users should note that the VEP will only look for overlaps (both exact and inexact) with these annotations; for example, any sequence in a GTF file will not be taken into account." (http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html)
I am using VEP 79 to annotate a VCF against allele counts from two VCF files using --custom. One VCF file is the ExAC r0.3 file (ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz); this can contain multiple alternate alleles separated by a comma, e.g.
1 20395401 rs11573185 C A,G,T 6372227.62 PASS AC=7149,3,1
The second VCF file is 'normalised' so that a variant location with two alternate alleles is represented as two separate lines, each with only one alternate allele.
1 20395401 . C A 709 . AC=2154
1 20395401 . C G 95 . AC=1
I have a sample with a heterozygous C/A genotype. The INFO tag added for ExAC is "ExAC.r0.3_AC=7149,3,1", i.e. it adds the allele count for all alternate alleles, although only one is observed in this sample. The tag AC=1 is added for the other database, i.e. it adds the allele count for the G allele, which is not observed, rather than the A allele, which is.
Is there a way to make VEP only report the annotations for the alternate allele(s) observed in the input VCF?
I am running variant_effect_predictor.pl with options `--check_existing` and `--check_alleles` and custom annotation is performed using e.g. `--custom ExAC.r0.3.sites.vep.vcf.gz,ExAC.r0.3,vcf,exact,0,AF,AC,AN`
Many thanks for your advice,
Katherine
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