PED-MAP

PED-MAP to VCF

./plink --file input_file --recode vcf --out output_file

PED-MAP to RAW

./plink --file input_file --recodeA --out output_file

PED-MAP to BED-BIM-FAM

./plink --file input_file --make-bed --out output_file

PED-MAP to GEN-SAMPLE

./plink --file  input_file --export oxford --out output_file

PED-MAP to 23andme

#Input file should not include extension
1. Convert PED-MAP to BED-BIM-FAM  --> PED-MAPtoBED-BIM-FAM()
./plink --file input_file --make-bed --out output_file

2. Convert BED-BIM-FAM to 23andme --> BED-BIM-FAMto23andme()
See BED-BIM-FAMto23andme

PED-MAP to AncestryDNA

#Input file should not include extension
1. Convert PED-MAP to VCF --> PED-MAPtoVCF()
./plink --file input_file --recode vcf --out output_file

2. Convert VCF to AncestryDNA --> VCFtoAncestryDNA()
See VCFtoAncestryDNA

PED-MAP to HAPS-LEGEND-SAMPLE

#Input file should not include extension
1. Convert PED-MAP to VCF --> PED-MAPtoVCF()
./plink --file input_file --recode vcf --out output_file

2. Convert VCF to HAPS-LEGEND-SAMPLE --> VCFtoHAPS-LEGEND-SAMPLE()
bcftools convert output_file.vcf  -h  output_file2