[ensembl-dev] Output format

Will McLaren wm2 at ebi.ac.uk
Tue Jun 30 10:04:31 BST 2015


Hi Jennifer,

VEP supports writing output in VCF format, just add --vcf to your command
line (1).

You can also track which allele each "chunk" of output corresponds to with
--allele_number (2)

Regards

Will McLaren
Ensembl Variation

1:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_vcf
2:
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_allele_number

On 30 June 2015 at 02:02, Jennifer Yen <jennifer.yen at personalis.com> wrote:

> Hi Ensembl Team,
>
> Is there a flag for including the original vcf position and allele in the
> vep output? For indels the output positions change (specified over a range,
> rather than the start position in the vcf) and the reference allele is
> never in the output.  This would be useful for cross-referencing with
> different files using the positions as identifiers in the vcf.
>
> Thanks,
> Jenn
>
> ------------------------------
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> This message may contain privileged and / or confidential  information. If
> you are NOT the intended recipient of this message, copying, printing,
> disseminating, forwarding or any other use or action derived from its
> content is strictly prohibited. Please notify the sender immediately by
> e-mail if you have received this e-mail by error and delete this e-mail
> from your system. If you received the email by error and this message
> contains patient information, please report the error by contacting the
> Personalis Clinical Laboratory at clinical at personalis.com.
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150630/b1591d64/attachment.html>


More information about the Dev mailing list