calculate LOD between markers
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5.8 years ago
l0o0 ▴ 220

I am building a genetic map using joinmap4 with a F1 population of 148 samples, including 20k snp markers.
Now, I am trying to filter adjacent markers whose LOD is less than 2.

I know LOD can be calculated in joinmap, but it is quite a large date for joinmap to do that. So I am looking for some tools to do this job. LDhat is quite popular, but it is hard for me to convert snp data in joinmap format to LDhat input format.

May be there is a easy way to covert these data, or find a another soft to calculate LOD for these snp markder ?

data set like:

scaffold267.0_1047926   <hkxhk> hk      hk      hk      hk      hk      hk       ...
scaffold874.0_354096    <hkxhk> hk      hk      hk      hk      hk      hk      ...
scaffold96.0_29235      <nnxnp> np      np      nn      nn      nn      np     ...
scaffold312.0_749469    <hkxhk> hk      hk      kk      kk      hk      kk      ...

SNP DNA genetic • 1.4k views