example of a snakemake dedicated to variant calling.

TODO:

Refine freebayes params

VCF filter.

SNPeff

Example of a snakemake dedicated to variant calling.
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This pipeline does the variant calling of a bam file. The first rule is markDuplicate. It is an optional rule. You must indicate in the config file if you wish to activate this rule. (true/false)

The second rule indexes your bam file. And finally, the last rule call freebayes to detect snp and indel variants.

TODO:
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- Mapping rule ?

- Refine freebayes params

- VCF filter.

- SNPeff

Add information about the pipeline.
Add information about the pipeline.
