Qiuni Yang

Thank you! I figured it out

Hi everyone, I'm encountering an issue when exporting a VCF file from TASSEL and using it as input in LepMap3. Specifically, I’m wondering how LepMap3 handles the nucleotide codes (A/T/C/G…) in the VCF file and converts them into numerical haplotype codes. After processing, I open the output file in R and see genotypes represented by numeric codes (like 11, 12, 21, 22.....). However, the numeric codes vary each time for the same marker and individual, even though I’m using the same VCF and pedigree...