Closed AprilYUZhang closed 4 weeks ago
$ cat pedigree.txt Mother 0 0 Father 0 0 Progeny Father Mother
$ cat genotype.txt Mother 0 0 0 0 0 0 Father 2 2 2 2 2 2 Progeny 1 1 1 1 1 1
AlphaPeel -ped_file pedigree.txt -geno_file genotype.txt -out_file test -geno_prob -phased_geno_prob -seg_prob
$ cat test.phased_geno_prob.txt Father 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Father 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Father 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Father 0.9999 0.9999 0.9999 0.9999 0.9999 0.9999 Mother 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Mother 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Mother 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Mother 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Progeny 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Progeny 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Progeny 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Progeny 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
$ cat test.geno_prob.txt Father 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Father 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 Father 0.9999 0.9999 0.9999 0.9999 0.9999 0.9999 Mother 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Mother 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 Mother 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Progeny 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Progeny 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Progeny 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
cat test.seg_prob.txt Father 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Father 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Father 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Father 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Mother 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Mother 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Mother 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Mother 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Progeny 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Progeny 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Progeny 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500 Progeny 0.2500 0.2500 0.2500 0.2500 0.2500 0.2500
We don't have any info on which allele was actually transmitted from mother to progeny and father to progeny, so this is all correct.
AlphaPeel -ped_file pedigree.txt -geno_file genotype.txt -out_file test -geno_prob -phased_geno_prob -seg_probWe don't have any info on which allele was actually transmitted from mother to progeny and father to progeny, so this is all correct.