Segregation file

Input file

Input for hybrid mode imputation. Same format as the output.

Output file

The .seg_prob.txt file contains segregation probabilities for each individual. There are four lines per individual, corresponding to the four possible patterns of segregation (inheritance):

1. The grand paternal allele from the father and the grand paternal allele from the mother: \(Pr(F_{p,-} \& M_{p,-})\),

2. The grand paternal allele from the father and the grand maternal allele from the mother: \(Pr(F_{p,-} \& M_{-,m})\),

3. The grand maternal allele from the father and the grand paternal allele from the mother: \(Pr(F_{-,m} \& M_{p,-})\), and

4. The grand maternal allele from the father and the grand maternal allele from the mother: \(Pr(F_{-,m} \& M_{-,m})\).

The symbols above mean the following: Pr() probability, F father, M mother, p paternal allele, m maternal allele, and - the allele that was not inherited.

The first value in each line is the individual ID. The remaining values are segregation probabilities at each locus.

Example with four individuals and four loci:

id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id1 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id2 0.2500 0.2500 0.2500 0.2500
id3 0.3356 0.3894 0.5000 0.4390
id3 0.1644 0.1106 0.0000 0.0610
id3 0.3356 0.3894 0.5000 0.4390
id3 0.1644 0.1106 0.0000 0.0610
id4 0.2046 0.1953 0.2760 0.3914
id4 0.2954 0.3047 0.2240 0.1086
id4 0.2046 0.1953 0.2760 0.3914
id4 0.2954 0.3047 0.2240 0.1086