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Depth-weighted De-Mixing
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lineage Misc? #171

Closed ybdong919 closed 11 months ago

ybdong919 commented 11 months ago

what is the meaning of lineage "Misc" in the out file of freyja?

dylanpilz commented 11 months ago

When calling freyja demix using the --depthcutoff option, sites with coverage below the user-specified cutoff value are excluded from the barcodes matrix. This then results in some lineage having identical barcodes, which is then resolved via shared ancestry between "identical" lineages. In some cases, (typically with poor coverage and high depthcutoff, it is impossible to find a clear recent common ancestor for these groups of lineages. Most commonly, this occurs when multiple distinct recombinant lineages are grouped together, or recombinant lineages are grouped with non-recombinant lineages. In such cases, we find it most informative to avoid checking the recombinant parents for shared ancestry, and instead designate the group with "Misc".

To see how the original lineages have been grouped into higher-order classifications, you can check the collapsed_lineages.yml file that is produced when running demix with the depthcutoff option.

Let me know if you have any further questions or if I can clarify anything! -Dylan

tibitoy commented 11 months ago

What if you get this result without using the -depthcutoff option? I've seen " miscBA1BA2Pre10k" or "miscDeltaBA1Post11k" in some of my samples but I don't use that option. Not sure how to interpret this.

joshuailevy commented 11 months ago

Oh, this is a slightly different "misc" actually, resulting from some of the naming conventions used in the UShER tree. These "misc" lineages are undesignated sub-clades that have been annotated in the global phylogeny.

If you're using a more recent version of Freyja, these lineage barcodes should be dropped by default. However, if you're constructing your own barcodes (either via an older version of Freyja or using the --buildlocal option) with the --noncl flag, these will still pop up.

tibitoy commented 11 months ago

Thanks for the help! I just used "freyja update" and reran it on some samples but am still seeing "miscDeltaBA1Post11k". Is there something else I need to do to update to the most recent version of Freyja?

On Mon, Aug 21, 2023 at 3:36 PM Josh Levy @.***> wrote:

Oh, this is a slightly different "misc" actually, resulting from some of the naming conventions used in the UShER tree. These "misc" lineages are undesignated sub-clades that have been annotated in the global phylogeny.

If you're using a more recent version of Freyja, these lineage barcodes should be dropped by default. However, if you're constructing your own barcodes (either via an older version of Freyja or using the --buildlocal option) with the --noncl flag, these will still pop up.

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joshuailevy commented 11 months ago

Running freyja update will only update the barcodes, it won't actually update Freyja itself. To do that you'll need to update the package, which will depend on how you installed Freyja. Assuming you installed via conda, you'll just need to install a more recent version of the package (most recent release is v1.4.5).

I'll close this issue, but let us know if that doesn't work for you!