[ensembl-dev] Fasta index issue with VEP82

[Alex Beesley]

Hi Will


Yup I am using the latest version (82) but I actually had considerable
trouble using VEP at all with the GRChr37
fasta downloaded via the API, and in the end had to use the -NO_HTSLIB
flag. Doesn¹t resolve the LoF problem though.


Cheers
Alex





On 22/10/2015 4:44 pm, "dev-bounces at ensembl.org on behalf of
dev-request at ensembl.org" <dev-bounces at ensembl.org on behalf of
dev-request at ensembl.org> wrote:

>------------------------------
>
>Message: 4
>Date: Thu, 22 Oct 2015 09:44:24 +0100
>From: Will McLaren <wm2 at ebi.ac.uk>
>Subject: Re: [ensembl-dev] Loftee and VCFCols Difficulties via port
>	3337
>To: Ensembl developers list <dev at ensembl.org>
>Message-ID:
>	<CAMVEDX2xmJaijWZsbHr4xWLWOZu0Geukcn2Ph5a9oZgk61Spvg at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Alex,
>
>Are you using the latest version of VEP? We have in version 82 an
>alternative FASTA indexer that is more robust to index corruption issues;
>it is also faster and allows you to use bgzipped FASTA files which take up
>much less disk space.
>
>http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html
>
>Regards
>
>Will McLaren
>Ensembl Variation