Entering edit mode
2.9 years ago
S. Roa
▴
10
Hello everyone!
I have a complex cattle pedigree in a .ped file, plink formatted, and I succesfully ran it in PedPhase. Pedigree: 1 family, 79 individuals, 40 founders, 50 SNP's.
I need to run that file in other algorithms for phasing, like Beagle, ShapeIt, or Whatshap. I'm a really beginner and would like some guidance on how to proceed, as I only have the .ped file. Can I run the other algorithms with just the .ped file? (I don't have the .map file)
In case it is possible, how can I convert the .ped file to beagle, or vcf format? I need to compare accuracy and run time of several algorithms.
I would really appreciate any guidance! Thank you for your help!
