Aaron Petkau

See https://github.com/tseemann/snippy/issues/501#issuecomment-1083236553

Try version `5.0` of snpeff instead: ``` mamba create --name snippy snippy snpeff==5.0 ``` For using the latest version of snpEff it looks like Java 12 is not available in...

If you wanted to operate directly on the VCF files you could use `bcftools isec`: https://samtools.github.io/bcftools/bcftools.html#isec

You might try making use of mamba instead of conda, which can be faster at resolving environments. That is `conda install mamba` and `mamba install snippy`.

You will likely want to install `snippy` to it's own conda environment to avoid Perl dependency mismatches, e.g.,: ```bash conda create --name snippy snippy conda activate snippy ``` Alternatively, I've...

@Jeewan-Thapa have you configured the bioconda channels https://bioconda.github.io/user/install.html#set-up-channels ?

Yes, you will need to do that. On Thu., Aug. 26, 2021, 7:36 p.m. Jeewan-Thapa, ***@***.***> wrote: > Thanks @apetkau , No I haven't. Do I need to > set-up...

That looks good to me. Now you can run `conda create --name snippy snippy`.

That's great. I'm glad to hear it's working. Yes, you will have to run `conda activate snippy` first before running `snippy` (and switch to a different environment for other software)....

Hello @ireneortega, Which unknown mutations are these? One possible reason is that the PointFinder database has been updated away from the default version. You can check the PointFinder database version...