Hi Pasi,
I don’t understand where the pedigree file comes from, I have GBS data and I used STACKS to get files .vcf, .ped and .map but I don’t know how to get the pedigree file. In addition, I have doubts about how should be configured the pedigree file because my populations are haploid and from strictly maternal inheritance.
I read in an article that the pedigree file should be configured as follows: maternal genotype to 1/2, the paternal genotype to 1/1, and missing genotype to 0/0, is correct?
If is right, how can I get the pedigree file with these characteristics?
Thanks
Xochitl
Last edit: Xochitl Granados 2023-09-28
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Hi Pasi,
I don’t understand where the pedigree file comes from, I have GBS data and I used STACKS to get files .vcf, .ped and .map but I don’t know how to get the pedigree file. In addition, I have doubts about how should be configured the pedigree file because my populations are haploid and from strictly maternal inheritance.
I read in an article that the pedigree file should be configured as follows: maternal genotype to 1/2, the paternal genotype to 1/1, and missing genotype to 0/0, is correct?
If is right, how can I get the pedigree file with these characteristics?
Thanks
Xochitl
Last edit: Xochitl Granados 2023-09-28