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Further Information

Hello,

We are working on a project where we plan on doing variant calling on single or double digest RAD-seq data. Our pipeline architecture has in mind using the suite Stacks to get VCF files. So far, i havent found any module, workflow or resource in the nf-core website/modules repo where this software is used.

Stacks has a set of tools to do either a denovo or reference guided analysis. We plan on doing a reference guided analysis. To that end we plan on creating a stacks module focused on the "ref_map.pl" script, which gets a bunch of bam files and does the whole variant calling. "ref_map" is in itself a sort of wrapper for two other tools of the suite, "gstacks" and "populations" and is possible to pass custom parameters from ref_map to either/both "gstacks" and "populations" (im yet to find how to do that in nextflow cleanly).

I already made a fork and im working on the module,

Thank you, im open to receive your feedback

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