PED-MAP
=======

PED-MAP to VCF
------------------------


.. code-block:: console

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

PED-MAP to RAW
------------------------

.. code-block:: console

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



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


.. code-block:: console

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



PED-MAP to GEN-SAMPLE
------------------------


.. code-block:: console

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



PED-MAP to 23andme
------------------------


.. code-block:: console

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


.. code-block:: console

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


.. code-block:: console

   #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