Feature request: min_samples_snp parameter

dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets

http://ipyrad.readthedocs.io

GNU General Public License v3.0

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Feature request: min_samples_snp parameter #421

Open isaacovercast opened 3 years ago

isaacovercast commented 3 years ago

When filtering the unlinked snps files it would be useful to have a parameter to control how sites with indels are treated. Maybe the filter can just ignore all indel sites when filtering unlinked snps? Or maybe it can set a threshold minimum number of samples per snp analogous to the min_samples_locus. Maybe it would even be a 'hackersonly' parameter. Just an idea.

eaton-lab commented 3 years ago

This is implemented in the snps_extracter tool used in ipyrad.analysis. We could either (1) advise users to just use the ipa tools if they want to implement this filter; or (2) maybe it is easy to implement as a hackers option like you said. We'd have to look into it on the latter front...