I'm working with GBS data in JoinMap v5. On most of my chromosomes, JoinMap works just fine and gives me a map output. However, on several chromosomes, when I go to construct the map, I get the error "unsuccessful in linkage phase determination error." This error does not appear in the manual and Googling the phrase has not turned up any results.
There are no differences which I can detect in the chromosomes in question. The marker format is identical and there are no issues with incorrectly coded SNP calls. The input data does not include phase information, but this has not been an issue with the other chromosomes.
In the information window following receipt of the error it states:
- unsuccessful in linkage phase determination
- current status:
- groups between which the linkage phases could not be determined:
- group: [lists out all the SNPS]
However, there is only one group, so it cannot be failing to find phasing between groups.
Any help with determining what the error means and how I should go about addressing it would be greatly appreciated.
The "unsuccessful in linkage phase determination error" in JoinMap typically occurs when the software is unable to determine the linkage phases between markers in a particular group. This error can occur for a variety of reasons, including errors in the input data or problems with the algorithm used to determine the linkage phases.
One possible cause of the error in your case could be the presence of errors in the input data. For example, if you have missing data or incorrect genotype calls for certain markers, this could prevent JoinMap from accurately determining the linkage phases. It is worth checking the input data carefully to ensure that there are no errors or inconsistencies that could be causing the error.
Another potential cause of the error could be problems with the algorithm used to determine the linkage phases. JoinMap uses a variety of algorithms to determine the linkage phases between markers, and if there are issues with the algorithm, it may be unable to accurately determine the linkage phases. In this case, you may need to try using different algorithms or adjusting the algorithm settings to see if this helps resolve the error.
It is also worth noting that the error may be occurring because there is insufficient information in the input data to accurately determine the linkage phases. If the markers are not evenly spaced or there are relatively few markers in the group, this may make it difficult for JoinMap to accurately determine the linkage phases. In this case, you may need to add more markers to the group or use a different method to construct the map.
Overall, it is important to carefully review the input data and the settings used in JoinMap to determine the cause of the "unsuccessful in linkage phase determination error" and to identify the appropriate solution. If the error persists after trying these suggestions, it may be helpful to seek additional guidance or assistance from an expert in the field.
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