recipe bioconductor-asafe

Ancestry Specific Allele Frequency Estimation







biotools: asafe, doi: 10.1093/bioinformatics/btw220

Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.

package bioconductor-asafe

(downloads) docker_bioconductor-asafe



depends r-base:




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 bioconductor-asafe

and update with::

   mamba update bioconductor-asafe

To create a new environment, run:

mamba create --name myenvname bioconductor-asafe

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 `bioconductor-asafe/tags`_ for valid values for ``<tag>``)

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