negative Fst scores

[dalloliogm]

Congratulations for the good work with this pipeline,

I've just run the tutorial, and saw that some positions have negative Fst values:

2       130041001       130042000       4       -0.00102404     -0.00132401
2       130042001       130043000       5       -0.000330858    0.00367176

This is a problem of vcftools and it may be in the scope of the pipeline to fix it; however, in principle negative Fst scores should not be possible, and are considered to be errors due to rounding when calculating the scores. Maybe it would be useful to add an option to convert all the negative Fst scores to 0? Alternatively, it may be useful to note this in the documentation.

Best
Gio

[murraycadzow]

Hi Gio,

Thanks for the suggestion. I was aware of the negative Fst values that VCFtools generates and when I use them in my analysis in R I do just as you mention and set all negative scores to 0. We froze features for selectionTools1.0 but I am slowly adding additional features in the selectionTools1.1 branch so if I might add a parser to change the Fst results.

I'll at least update the documentation to raise awareness for the issue

thanks
Murray