I have a vcf file containing data on 9 individuals with 1006 and 1007 designated as parents while the others (1001-1005 and 1007-1008) are their offspring. At position 142840 the genotype is as follows: 1/1, 0/1, ,0/1, 0/1, 0/1, 1/1, 0/1, 0/1, 1/1 hence the parents have genotype of 1/1 and 1/0. I run the following command:
java -jar beagle.22Jul22.46e.jar gt=100family_chr6.vcf ped=100family_info.txt out=100family_phased
and get the phase data that looks like this: chr6 142840: 1|1 1|0 0|1 1|0 0|1 1|1 1|0 0|1 1|1
However this outcome doesn't make sense because the expected possibilities should be 1|1 and 1|0 with 0|1 being improbable given the parents has genotype of 1|1 and 1|0. Why do I get this error? Is it possible the problem is with the info file? the file looks like this:
It seems that the phasing process is failing to recognize the parents as such. How can I solve this issue?
