BED-BIM-FAM
===========

BED-BIM-FAM to PED-MAP
------------------------


.. code-block:: console

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

   

BED-BIM-FAM to RAW
------------------------

.. code-block:: console

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



BED-BIM-FAM to VCF
------------------------


.. code-block:: console

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



BED-BIM-FAM to GEN-SAMPLE
------------------------------


.. code-block:: console

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



BED-BIM-FAM to 23andme
------------------------


.. code-block:: console

   #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
------------------------------


.. code-block:: console

   #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
--------------------------------------


.. code-block:: console

   #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