GEN-SAMPLE
==========

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


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   

GEN-SAMPLE to RAW
------------------------

.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --recodeA --out output_file2


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


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --make-bed --out output_file2


GEN-SAMPLE to VCF
------------------------


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --recode vcf --out output_file2



GEN-SAMPLE to 23andme
------------------------


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --recode vcf --out output_file2
   1. Convert VCF to 23andme --> VCFto23andme()
   See VCFto23andme


GEN-SAMPLE to AncestryDNA
------------------------------


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --recode vcf --out output_file2
   1. Convert VCF to 23andme --> VCFto23andme()
   See VCFto23andme
   2. Convert 23andme to AncestryDNA --> 23andmetoAncestryDNA()
   See 23andmetoAncestryDNA

GEN-SAMPLE to HAPS-LEGEND-SAMPLE
--------------------------------------


.. code-block:: console

   ./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
   ./plink --file output_file --recode vcf --out output_file2
   bcftools convert output_file2.vcf  -h  output_file3