Creating Pedigree Files with F2 Generation Population

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Creating Pedigree Files with F2 Generation Population

Forum: General Discussion

Creator: 康明明

Created: 2025-03-04

Updated: 2025-03-04

康明明 - 2025-03-04

Dear Pasi，
Hello，I’m working with an F2 hybrid plant population, and I’ve already generated an SNP dataset for 218 samples using GATK. However, I’m stuck on creating the pedigree file for LepMap3 because I don’t have any parental data for my samples. What I do know is that both parents are homozygous, so I’ve filtered the VCF file to retain only biallelic SNP sites. Below is a portion of the VCF file, and I’d greatly appreciate it if you could help me write a pedigree file tailored to this VCF.
Wishing you all the best in life!

1.vcf

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康明明 - 2025-03-04

Oh, I think I've got the pedigree file sorted out. It seems to be fine for now.

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