Activity for Etienne Dvrk
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Etienne Dvrk posted a comment on discussion General Discussion
Dear Pasi, Thank you very much for your response and your suggestions. Increasing phasingIterations has no effect in my case. Anyway the distances computed with the physical order seem fine. By the way, I could not find an exhaustive documentation of the parameters for each command. For example I had to search in this forum to know if OrderMarkers2 uses Haldane or Kosambi mapping function by default. Does this documentation exist somewhere? Etienne D.
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Dear Pasi, I have a question regarding what to trust more between likelihood and map length. My data consists of 2 half-sibs families (two crosses with one parent in common) (~2x170 individuals, ~5000 markers). I already built parental maps with another software and obtained good results, with only a handful of discrepancies with the physical order. Then I used LepMAP to get a consensus map with all markers together. First I directly input the assumed physical order like this: java -cp ./bin OrderMarkers2...
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