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Rule Call Graph

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Lucas Czech edited this page Jan 13, 2021 · 10 revisions

The default setup, using trimmomatic for read trimming, bwa mem for mapping, and GATK HaplotypeCaller for calling, has the following rule dependencies and data flow:

Rule call dependency graph

If configured to use different tools, such as bowtie2 and bcftools call, the graph might look different, depending on which extra steps are needed for these tools.

To get the rule dependency graph and the complete job call graph, use

snakemake --rulegraph | dot -Tsvg > rules.svg
snakemake --dag | dot -Tsvg > dag.svg

Note that you might need to specify the --directory in which your config.yaml is located for the above snakemake calls.

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