Script to transform vcf genotypes to a tped plink file
vcfToPlink file.vcf pedigreeFile plink
file.vcf is the vcf file, pedigree file is a csv with a header and columns FID, IID, FA, MO, SEX, STATUS where
- FID is the family id
- IID is the individual id
- FA is IID of the Father, 0 for unknown
- MO is the IID of the Mother 0 for unknown
- SEX 1 for Males and 2 for females
- STATUS 0 or 1, -9 for missing