I am working with the sex chromosome linkage map. In order to take into account sex linked markers, I used ZLimit=2. When I compare the genotypes before and after, I see the following change:
Genotypes before ParentCall:
father 1 2
mother 2 2
daughter 1 1
After using ZLimit=2, the daughter genotype has turned into 1 2. I was wondering how in later stages, these cases are recognized as sex linked and are not treated as an autosomal marker?
Thank you very much,
Best,
Homa
Last edit: Homa 2016-08-09
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X/ZLimit will convert sex inherited markers into autosomal like markers. There will be star in the output of ParentCall indicating the marker is converted.
Without ZXLimit, there would be Mendel errors in the data. Then either the marker would not be called or the parental or children's genotypes would be changed (in your case the mother to 1 2).
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
Thank you for the great software.
I am working with the sex chromosome linkage map. In order to take into account sex linked markers, I used ZLimit=2. When I compare the genotypes before and after, I see the following change:
Genotypes before ParentCall:
father 1 2
mother 2 2
daughter 1 1
After using ZLimit=2, the daughter genotype has turned into 1 2. I was wondering how in later stages, these cases are recognized as sex linked and are not treated as an autosomal marker?
Thank you very much,
Best,
Homa
Last edit: Homa 2016-08-09
Hello Homa,
Thank you for your email.
X/ZLimit will convert sex inherited markers into autosomal like markers. There will be star in the output of ParentCall indicating the marker is converted.
Without ZXLimit, there would be Mendel errors in the data. Then either the marker would not be called or the parental or children's genotypes would be changed (in your case the mother to 1 2).
Cheers,
Pasi