recipe clair3-trio

Clair3-Trio is a variants caller tailored for family trios from nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model that allows it to input all trio’s sequencing information and output all trio’s predicted variants within a single model, to perform far better variant calling. We also present MCVLoss, the first loss function that can improve variants calling in trios by leveraging the explicitly encoding of the priors of the Mendelian inheritance in trios. Clair3-Trio showed comprehensive improvement in experiments. It predicted much fewer Mendelian inheritance violation variations than current state-of-the-art methods.

Homepage:

https://github.com/HKU-BAL/Clair3-Trio

License:

BSD-3-Clause

Recipe:

/clair3-trio/meta.yaml

package clair3-trio

versions:

0.7-2,  0.7-1,  0.7-0,  0.6-1,  0.6-0,  0.5-0,  0.3-2,  0.3-1,  0.3-0, 

0.7-2,  0.7-1,  0.7-0,  0.6-1,  0.6-0,  0.5-0,  0.3-2,  0.3-1,  0.3-0,  0.2-0,  0.1-0

depends bzip2:

>=1.0.8,<2.0a0

depends cffi:

depends libgcc:

>=13

depends liblzma:

>=5.6.3,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.2.13,<2.0a0

depends numpy:

depends parallel:

20191122.*

depends pigz:

depends pypy3.6:

depends pytables:

depends python:

>=3.9,<3.10.0a0

depends python_abi:

3.9.* *_cp39

depends samtools:

1.15.1.*

depends tensorflow:

2.8.0.*

depends whatshap:

1.7.*

depends zstd:

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 clair3-trio

and update with::

   mamba update clair3-trio

To create a new environment, run:

mamba create --name myenvname clair3-trio

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/clair3-trio:<tag>

(see `clair3-trio/tags`_ for valid values for ``<tag>``)

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