From plink to GeneHunter format
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Entering edit mode
4 weeks ago
lucas_ ▴ 20

Hello, hope someone tried it before and could help me with this.

My dataset is in plink format (.bed, .bim, .fam). I am doing linkage analysis for MOD score using GeneHunter. i need to code .dat file:

4 0 0 5  << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.0 0.0 0  << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
1 2 3 4
1  2  << AFFECTATION, NO. OF ALLELES
0.9 0.1  << GENE FREQUENCIES
1  << NO. OF LIABILITY CLASSES
0.95 0.01 0.95
3  2
0.3 0.7
3  2
0.3 0.7
3  2
0.3 0.7
0 0
0.01 0.01 0.1
1 0.1 0.45  << REC VARIED, INCREMENT, FINISHING VALUE
  1. I tried mega2 to convert from plink format to genhunter format but not able to do it.
  2. Genhunter manual refers to use "output from the PREPLINK program" . some one before PREPLINK program ?
  3. Any ideas how to code or produce .dat file from plink formats ?

Thank you

linkage-analysis • 186 views
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