- recipe contatester
Compute the Allelic Balance of a sample from a VCF file.
Contatester computes the Allelic Balance of a sample from a VCF file, check if a cross human contamination is present and estimate the degree of contamination, using pegasus for high efficiency.
- package contatester¶
- depends bcftools:
- depends libgcc-ng:
- depends libstdcxx-ng:
- depends openmpi:
- depends python:
- depends python-pegasus-wms:
- depends python_abi:
- depends r-base:
- depends r-gridbase:
- depends r-gridextra:
- depends r-optparse:
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 contatester and update with:: mamba update contatester
To create a new environment, run:
mamba create --name myenvname contatester
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/contatester:<tag> (see `contatester/tags`_ for valid values for ``<tag>``)