recipe vcfsamplecompare

This script sorts and (optionally) filters the rows/variants of a VCF file (containing data for 2 or more samples) based on the differences in the variant data between samples or sample groups. Degree of "difference" is determined by either the best possible degree of separation of sample groups by genotype calls or the difference in average allelic frequency of each sample or sample group (with a gap size threshold). The pair of samples or sample groups used to represent the difference for a variant row is the one leading to the greatest difference in consistent genotype or average allelic frequencies (i.e. observation ratios, e.g. AO/DP) of the same variant state. If sample groups are not specified, the pair of samples leading to the greatest difference is greedily discovered and chosen to represent the variant/row.

Homepage:

https://github.com/hepcat72/vcfSampleCompare

License:

GNU

Recipe:

/vcfsamplecompare/meta.yaml

Links:

doi: 10.5281/zenodo.3565896

package vcfsamplecompare

(downloads) docker_vcfsamplecompare

versions:

2.013-2,  2.013-1,  2.013-0,  v2.008-1,  v2.008-0,  v2.006-0

depends perl:

>=5.32.1,<6.0a0 *_perl5

requirements:

additional platforms:

Installation

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 vcfsamplecompare

and update with::

   mamba update vcfsamplecompare

To create a new environment, run:

mamba create --name myenvname vcfsamplecompare

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 quay.io/biocontainers/vcfsamplecompare:<tag>

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

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Link to this page

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