[ensembl-dev] Retrieving Exac homozygous count through Rest interface

Will McLaren wm2 at ebi.ac.uk
Thu Jan 19 16:46:20 GMT 2017


Hello,

I'm afraid there's no way to do it through the REST interface.

The VEP command line tool will happily retrieve this info for you from the
ExAC VCF file using the --custom flag [1], though you will need to use the
new beta version [2] to do this:

perl vep.pl -i examples/homo_sapiens_GRCh38.vcf -custom
ExAC.0.3.GRCh38.vcf.gz,ExAC_VCF,vcf,exact,,AC_Hom

This will output it as a tab-delimited file with the data in the Extra
column. You can get the VCF from the Ensembl FTP site [3]

You could even have VEP map this to a field in your VCF:

perl vep.pl -i examples/homo_sapiens_GRCh38.vcf -custom
ExAC.0.3.GRCh38.vcf.gz,ExAC_VCF,vcf,exact,,AC_Hom -fields ExAC_VCF_AC_Hom
-vcf_info_field AC_Hom

Regards

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html
[2] : https://github.com/Ensembl/ensembl-vep
[3] : ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/

On 19 January 2017 at 14:57, Wolf Beat <Beat.Wolf at hefr.ch> wrote:

> Hi,
>
>
> is it somehow possible to retrieve the homozygous frequency/count from
> exac in the VEP tool available through the REST interface?
>
>
> You already get almost all information from exac, except the nomber of
> homozygotes (either as a number or as a frequency).
>
>
> Is it planned to add this information, or is it possible to retrieve it
> otherwise?
>
>
> Kind regards
>
>
> Beat Wolf
>
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