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Re: Bug#986141: ITP: snpeff -- genetic variant annotation and effect prediction toolbox

Hi Andreas,

Le 30/03/2021 à 13:07, Andreas Tille a écrit :
Hi Pierre,

very nice.  Seems you had some progress with this long term

Yes! It is almost ready and I'm happy about this :)

While we are at it: I had to package SnpEff separately from its companion SnpSift, as their source trees are now completely separated. Do you (or someone else) know if SnpSift would be important to package? Looking at the spreadsheet I am not sure it is worth packaging right now.

Thanks a lot


Best wishes,

On Tue, Mar 30, 2021 at 12:24:18PM +0200, Pierre Gruet wrote:
Package: wnpp
Severity: wishlist
Owner: Debian-med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : snpeff
   Version         : 4.3t
   Upstream Author : Pablo Cingolani <pcingola@users.sourceforge.net>
* URL             : https://pcingola.github.io/SnpEff/
* License         : LGPL-3
   Programming Lang: Java
   Description     : genetic variant annotation and effect prediction toolbox

SnpEff is a variant annotation and effect prediction tool. It annotates
and predicts the effects of variants on genes (such as amino acid

The inputs are predicted variants (SNPs, insertions, deletions and
MNPs). The input file is usually obtained as a result of a sequencing
experiment, and it is usually in variant call format (VCF).

SnpEff analyzes the input variants. It annotates the variants and
calculates the effects they produce on known genes (e.g. amino acid

This software is needed in many workflows in the Debian-med team. It will be
maintained inside the team.

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