[svtoolkit-help] Running GenomeSTRiP on non-human organism

[Ana P. <ana...@gm...>]

Dear Bob,

I have installed and run the test data for svtoolkit_2.00.1602 with no errors.

I work with a non-human female heterogametic (ZW) system and while reading the documentation under
http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html
on how to built a custom reference metadata bundle, I came across the following statement under the reference.ploidymap.txt section
"Currently, only organisms with a human-like XY sex determination system are fully supported."


My question is: what does this actually mean?

Does it mean that they are not supported just simply because there are no examples of any of them under your reference metadata bundles?
Or does it mean that for my runs to work I need to swap the Z for a X and the W for a Y when I make the ploidymap.txt?
Or does it mean that beyond swapping the letter (Z->X & W->Y) I also have to label males as females and females as males so that the predictions of a male heterogametic system match up with what I am feeding into it?

Finally, what would your predictions be if I dropped any W linked regions altogether from the analysis? Would a Z0 system be allowed? If so, how would I make the ploidymap be able to reflect this correctly?

Thank you in advance for the time spent,

All the best,

Ana