How to infer missing values with BEAGLE 4 with a pedigree file available?

Question

[wangjinpeng0225]

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
  singles: 1
  duos:    0
  trios:   0

This puzzled me a lot. Who can help me?

Answer 1

[robert.kwapich]

Hey, I also tried running beagle 4.0 (I know there is beagle 4.1 and 5, but this is the only beagle that uses family/pedigree data to impute missing genotypes, and I've had a lot of issues with polymutt).

I tried formatting my ped file differently. I've removed headline, I've used spaces or tab-delimit sign as column separators, I've ensured that the sample IDs are unique. There are no peeling errors, trees are easily constructed with Kinship2 package. Yet I get the same problem - for my set of 3k+ samples, I get the exact same number of "singles", despite the dataset being highly in the family (multiple families).

[linfengchen2019]

Hi, I got the same problem. Have you solved it later?