{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
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   },
   "source": [
    "# Annotate Putative Somatic Variants with CIViC and VEP"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Welcome back to OpenCAP Jupyter Notebooks! Here you can run pre-designed code to generate an output report for your variants. \n",
    "\n",
    "To run Jupyter notebook cells hold-down on \"shift\" and select \"enter\"."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Commands to annotate variants"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We have created a python script called identified_variants_to_annotation.py that will take in variants from the sequencing pipeline and output a document with annotation information. The output will include variant effect predictions and clinical interpretations of variants in cancer.\n",
    "\n",
    "Before running this cell, please upload your somatic variants to the home directory (see ReadTheDocs) and change the input variant list name to match your somatic variant list. You can run the cell by holding the \"shift\" key and selecting \"enter\"."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Variant annotation has been successfully completed!\n"
     ]
    }
   ],
   "source": [
    "#       #Python Script                         #Input Variant List          #Sample Name\n",
    "%run -i 'identified_variants_to_annotation.py' 'test_annotate_variants.tsv' 'SCLC_9'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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