BED-BIM-FAM

BED-BIM-FAM to PED-MAP

./plink --bfile input_file --recode --out output_file

BED-BIM-FAM to RAW

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

BED-BIM-FAM to VCF

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

BED-BIM-FAM to GEN-SAMPLE

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

BED-BIM-FAM to 23andme

#Input file should not include extension.
if not os.path.isdir("23andme"):
   os.mkdir("23andme")

#Extract id of each person
data = pd.read_csv(input_file+".fam",sep="\s+",header=None)
print(data)
data = data [[0,1]]
data.to_csv("./23andme/temp_samples.txt",header=False,index=False,sep=" ")

#Open that file
f = open("./23andme/temp_samples.txt", "r")
for x in f:

   #Write each person name in a specific file
   temp = open("./23andme/temp.txt", "w")
   temp.write(x)
   temp.close()

   #Extract each person from BED,BIM,FAM file and convert it to 23andme.
   os.system("./plink --bfile "+input_file.split(".")[0]+" --keep ./23andme/temp.txt --recode 23 --snps-only --out ./23andme/"+x.split(" ")[0]+"_"+x.split(" ")[0])

BED-BIM-FAM to AncestryDNA

#1. Convert BED-BIM-FAM to VCF --> BED-BIM-FAMtoVCF()
./plink --bfile input_file --recode vcf --out output_file

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

BED-BIM-FAM to HAPS-LEGEND-SAMPLE

#Input file should not include extension

#Convert BED-BIM-FAM to VCF --> BED-BIM-FAMtoVCF()
./plink --bfile input_file --recode vcf --out output_file

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