Phased genotype probabilities file

Input file

This file has four lines with phased genotype probabilities for each genotyped and phased individual; possibly from previous analyses. The four lines respectively correspond to probabilities for aa, aA, Aa, and AA phased genotypes. The file does not need to include all individuals present in other files. The first value in each line is the individual ID. The remaining values are phased genotype probabilities at each locus. These values are assumed without an error and used directly as individual’s phased genotype probability state. Only loci on one chromosome should be provided!

Example with four individuals and four loci:

id1 0.7912 0.0000 0.0000 1.0000
id1 0.1044 0.1090 0.2637 0.0000
id1 0.1044 0.1090 0.2637 0.0000
id1 0.0000 0.7820 0.4725 0.0000
id2 0.0000 0.0000 0.0000 0.0001
id2 0.3764 0.6611 0.0000 0.9628
id2 0.6236 0.3388 1.0000 0.0371
id2 0.0000 0.0000 0.0000 0.0000
id3 0.3784 0.2171 0.0000 1.0000
id3 0.4140 0.0000 0.0001 0.0000
id3 0.0000 0.4328 0.0000 0.0000
id3 0.2076 0.3500 0.9999 0.0000
id4 0.9999 0.0000 0.0000 1.0000
id4 0.0000 0.0000 0.2912 0.0000
id4 0.0000 0.0000 0.7088 0.0000
id4 0.0000 0.9999 0.0000 0.0000

Output file

The .phased_geno_prob.txt file contains phased genotype probabilities for each individual.

There are four lines per individual, corresponding to probabilities for aa, aA, Aa, and AA phased genotypes. The first value in each line is the individual ID. The remaining values are phased genotype probabilities at each locus.

Example with four individuals and four loci:

id1 0.7912 0.0000 0.0000 1.0000
id1 0.1044 0.1090 0.2637 0.0000
id1 0.1044 0.1090 0.2637 0.0000
id1 0.0000 0.7820 0.4725 0.0000
id2 0.0000 0.0000 0.0000 0.0001
id2 0.3764 0.6611 0.0000 0.9628
id2 0.6236 0.3388 1.0000 0.0371
id2 0.0000 0.0000 0.0000 0.0000
id3 0.3784 0.2171 0.0000 1.0000
id3 0.4140 0.0000 0.0001 0.0000
id3 0.0000 0.4328 0.0000 0.0000
id3 0.2076 0.3500 0.9999 0.0000
id4 0.9999 0.0000 0.0000 1.0000
id4 0.0000 0.0000 0.2912 0.0000
id4 0.0000 0.0000 0.7088 0.0000
id4 0.0000 0.9999 0.0000 0.0000

When working with the X chromosome, for a female individual, the interpretation is as for an autosomal chromosome above. For a male individual, the first line and the last line respectively correspond to a and A genotypes, with the middle two lines are placeholders.

Example with four individuals and their X chromosome genotypes at four loci:

id1 and id3 are males, while id2 and id4 are females:

id1 0.7912 0.2179 0.5274 1.0000
id1 0.0000 0.0000 0.0000 0.0000
id1 0.0000 0.0000 0.0000 0.0000
id1 0.2088 0.7820 0.4725 0.0000
id2 0.0000 0.0000 0.0000 0.0001
id2 0.3764 0.6611 0.0000 0.9628
id2 0.6236 0.3388 1.0000 0.0371
id2 0.0000 0.0000 0.0000 0.0000
id3 0.3784 0.2171 0.0001 1.0000
id3 0.0000 0.0000 0.0000 0.0000
id3 0.0000 0.0000 0.0000 0.0000
id3 0.6216 0.7829 0.9999 0.0000
id4 0.9999 0.0000 0.0000 1.0000
id4 0.0000 0.0000 0.2912 0.0000
id4 0.0000 0.0000 0.7088 0.0000
id4 0.0000 0.9999 0.0000 0.0000