[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

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

>>>> 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.
>>> I have seen it mentioned from time to time but I'm not sure whether it
>>> was just in connection with SnpEff.  Tony and Steffen (both in CC)
>>> might
>>> give some more informed answer to your question.
>> The bcbio devs answered this here
>> https://github.com/bcbio/bcbio-nextgen/issues/1832
>> where they look forward to exclusively use vcfanno to filter the
>> variants.
>> Maybe a pointer to https://tracker.debian.org/pkg/vcfanno should be
>> added
>> as a suggestion to snpeff?
> Thanks a lot for the link of this issue; I agree such pointer would
> certainly be useful. Are you suggesting to add a ``Suggests: vcfanno''
> to the d/control file of snpeff or did you have something else in mind?

No, that's it. I just took some freedom and toyed with the description a
bit more. Please have a look. You may want to shorten it a bit more. It
should be understandable, though.

Another tool that could substitute (semantically) SnpEff is VEP, i.e.
the variant effect predictor by the ensembl.org team. I do not think we
have packaged this yet, though.



Reply to: