Hi Pasi,
Could you give a brief description of how the minError parameter works? Does it make global adjustments based on the setting, or focus on markers with higher detected error rates? Also, would you expect a higher minError setting to potentially 'correct' true recombinants, or is it robust in only making changes to markers with genotyping errors? Thanks much!
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MinError sets the minimum error parameter for the underlying hidden Markov model.
It should be robust for recombinations that have supporting markers on both sides of the map, that is, the map ends might have some problems. It should also be more robust if there are multiple identical markers.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Pasi,
Could you give a brief description of how the minError parameter works? Does it make global adjustments based on the setting, or focus on markers with higher detected error rates? Also, would you expect a higher minError setting to potentially 'correct' true recombinants, or is it robust in only making changes to markers with genotyping errors? Thanks much!
Dear John,
Thank you for this question,
MinError sets the minimum error parameter for the underlying hidden Markov model.
It should be robust for recombinations that have supporting markers on both sides of the map, that is, the map ends might have some problems. It should also be more robust if there are multiple identical markers.
Cheers,
Pasi