recipe harvest-variants

Harvest Variants is a pipeline for variant calling on SARS-CoV-2 samples

Homepage:

https://gitlab.com/treangenlab/sars-cov-2-harvest-variants

License:

MIT

Recipe:

/harvest-variants/meta.yaml

package harvest-variants

Versions:

1.1.0-0,  1.0.1-0,  1.0.0-0,  0.3.1-2,  0.3.1-0,  0.0.4-0,  0.0.3-0

Depends:

• bcftools >=1.15

• bedtools >=2.30.0

• biopython >=1.79

• bwa >=0.7.17

• fastp >=0.22

• fastqc >=0.11.9

• lofreq >=2.1.3

• parsnp >=1.7.4

• python >=3.6

• pyvcf >=0.6.8

• samtools >=1.15

• snpeff >=5.1

• sra-tools 2.10.9.*

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install harvest-variants

and update with:

conda update harvest-variants

or use the docker container:

docker pull quay.io/biocontainers/harvest-variants:<tag>

(see harvest-variants/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

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