Demix low cov grouping - Githubissues

andersen-lab / Freyja

Depth-weighted De-Mixing

BSD 2-Clause "Simplified" License

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Closed dylanpilz closed 1 year ago

dylanpilz commented 1 year ago

Adds --grouplineages option to demix and boot, which drops mutations from df_barcodes at sites with depth <= covcut (coverage estimation cutoff). Additionally drops lineages containing low-coverage mutations.
Now handles cvxpy.error.SolverError (#137)

dylanpilz commented 1 year ago

Replaces --grouplineages and --groupingthresh parameters with --depthcutoff (default 0) in demix and boot.
Performs phylogenetic grouping of lineages containing SNVs at sites with coverage below depthcutoff