ex-282 (cgates/jebene): Refined quick start

doc/include_quickstart.rst

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+.. include:: ../examples/QUICKSTART.rst

examples/QUICKSTART.rst

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+===========
+Quick Start
+===========
+This is a simple tutorial on how to use the 4 basic Jacquard commands.
+
+
+#. Install Jacquard per instructions in :ref:`Installing Jaquard`.
+
+
+#. Expand the examples.zip [LINK THIS] file to you home directory (or other
+   directory of your choice).
+
+   The examples directory contains sample input VCFs from 5 patients run with 3
+   variant callers. The input VCFs are based on a subset of actual variant calls
+   from clinical data; the samples were deidentified and VCF positions have
+   been randomized to prevent downstream identification. As a result of
+   randomization, the sample VCF reference calls at a specific position don't
+   always match the base calls from a reference sequence.
+
+   Along with the inputs, the example dierctory contains output from each
+   Jacquard command, as explained below.
+
+
+
+
+
+#. Create an output directory.
+
+
+#. translate
+   The translate [LINK] command creates new VCFs adding a controlled
+   vocabulary of new FORMAT tags.
+
+   ``$jacquard translate examples/00-input_vcfs/ <output_dir>``
+
+
+#. merge
+   The merge [LINK] command integrates a directory of VCFs into a single VCF.
+
+   ``$jacquard merge examples/01-translated/ <output_vcf_file>``
+
+
+#. summarize
+   The summarize [LINK] command adds new INFO fields and FORMAT tags that
+   combine variant data from the merged VCF.
+
+   ``$jacquard summarize examples/02-merged.vcf <output_vcf_file>``
+
+
+#. expand
+   The expand [LINK] command explodes a VCF file into a tab-separated file.
+
+   ``$jacquard expand examples/03-summarized.vcf <output_tsv_file>``
+
+
+Refer to overview [LINK] for more information on Jacquard.