I am new to Beagle. I want to infer missing values in my GBS data with Beagle 4. I want to construct a linkage map with a family of two parents and 100 offspring. I constructed sequencing libraries with the GBS strategy and got sequence data with many missing values in many individuals. I want to impute the missing values with Beagle but I cannot make it work. I made a pedigree file in this format:
3 100 252 251
3 101 252 251
But it cannot be read into the program. The log file read like this:
reference samples: 0
target samples: 1
This puzzled me a lot. Who can help me ?