recipe vsnp

Rapidly call, validate, and compare SNPs from FASTQ files in a timely manner utilizing large data sets.






package vsnp

(downloads) docker_vsnp



depends abyss:

depends biopython:

depends bwa:

depends dask:

depends freebayes:

depends humanize:

depends matplotlib-base:

depends pandas:

depends picard:

depends py-cpuinfo:

depends pysam:

depends python:


depends pyvcf:

depends raxml:

depends regex:

depends samtools:

depends scikit-allel:

depends vcflib:

depends xlrd:

depends xlsxwriter:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install vsnp

and update with::

   mamba update vsnp

To create a new environment, run:

mamba create --name myenvname vsnp

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `vsnp/tags`_ for valid values for ``<tag>``)

Download stats