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

[Pierre Gruet <pgt@debian.org>]

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
> goal!

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
>
>       Andreas.

Best wishes,
Pierre

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