I was asked to run the linkage analysis using CRIMAP as well as Lepmap2.
For CRIMAP, I had to use PedPhase 3.0 to put together closely linked markers to create haplotypes when there is no recombination.
With Lepmap2, when I run it for LOD => 3, I get male and female map of 121 and 91 cMs. With CRIMAP, when I run it for LOD => 5, I get 125 and 92 cMs for male and female maps. When I decrease LOD => 3 in CRIMAP, my map length increases to 155 and 113 cMs for males and females. I see the start and end of the map are where the increase has occurred.
I was wondering whether you have any experience with this?
Thank you,
Homa
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I might be biased here but I answer anyway. Maybe lower LOD score adds more erroneous markers to linkage groups? LM is quite robust to genotyping errors and reduces map inflation caused by them.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
I was asked to run the linkage analysis using CRIMAP as well as Lepmap2.
For CRIMAP, I had to use PedPhase 3.0 to put together closely linked markers to create haplotypes when there is no recombination.
With Lepmap2, when I run it for LOD => 3, I get male and female map of 121 and 91 cMs. With CRIMAP, when I run it for LOD => 5, I get 125 and 92 cMs for male and female maps. When I decrease LOD => 3 in CRIMAP, my map length increases to 155 and 113 cMs for males and females. I see the start and end of the map are where the increase has occurred.
I was wondering whether you have any experience with this?
Thank you,
Homa
Dear Homa,
Thank you for your email.
I might be biased here but I answer anyway. Maybe lower LOD score adds more erroneous markers to linkage groups? LM is quite robust to genotyping errors and reduces map inflation caused by them.
Cheers,
Pasi