recipe covsnap

Coverage inspector for targeted sequencing QC (hg38)

Homepage:

https://github.com/enes-ak/covsnap

Documentation:

https://github.com/enes-ak/covsnap/blob/main/README.md

License:

MIT / MIT

Recipe:

/covsnap/meta.yaml

covsnap computes per-target and per-exon depth metrics from BAM/CRAM files, producing a machine-readable raw TSV and a human-readable interpreted report with PASS/FAIL classifications. Supports gene symbols, genomic regions, and BED files as input. Ships with a bundled GENCODE v44 hg38 gene index — no internet or GTF files required at runtime.

package covsnap

(downloads) docker_covsnap

versions:

0.1.0-0

depends htslib:

>=1.17

depends numpy:

>=1.24

depends pysam:

>=0.22

depends python:

>=3.9

depends samtools:

>=1.17

depends tabix:

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 covsnap

and update with::

   mamba update covsnap

To create a new environment, run:

mamba create --name myenvname covsnap

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/covsnap:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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