Added an example for students to work through.

ncgr · Feb 6, 2025 · 3aa82b1 · 3aa82b1
1 parent 59174a3
commit 3aa82b1
Showing 1 changed file with 24 additions and 4 deletions.
diff --git a/module_notebooks/05-variant-calling-with-vg.ipynb b/module_notebooks/05-variant-calling-with-vg.ipynb
@@ -90,7 +90,8 @@
     "The parameters:\n",
     "\n",
     "-k  The read support file to read in  \n",
-    "-t  The number of threads"
+    "-t  The number of threads\n",
+    "The graph"
    ]
   },
   {
@@ -99,7 +100,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!vg call S288C.xg -k S288C.SK1.illumina.pack -t 4 > S288C.SK1.illumina.graph_calls.vcf"
+    "!vg call -k yprp.chrVIII.pggb.mapped.pack -t 4 yprp.chrVIII.pggb.giraffe.gbz > yprp.chrVIII.pggb.graph_calls.vcf"
    ]
   },
   {
@@ -109,11 +110,24 @@
     "<div class=\"alert alert-block alert-info\"> <b>Try this:</b>  \n",
     "    <ul>\n",
     "        <li>Create a blank code cell below.</li>\n",
-    "        <li>Align the SK1 reads to the graph created directly from the full genome (yprp.fullgenome.pggb.giraffe.gbz).</li>\n",
-    "        <li>Align the SK1 reads to the graph created by combining the 16 chromosomal subgraphs (yprp.allchrs.pggb.giraff.gbz).</li>\n",
+    "        <li>Call variants in the full genome graph by computing read support and then generating a vcf file.</li>\n",
     "    </ul>"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<details>\n",
+    "<summary>Click for help</summary>\n",
+    "<br>\n",
+    "!vg pack -x yprp.fullgenome.pggb.giraffe.gbz -g SK1xyprp.fullgenome.pggb.mapped.gam -Q 5 -s 5 -o yprp.fullgenome.pggb.mapped.pack -t 4   \n",
+    "\n",
+    "    <br>\n",
+    "!vg call -k yprp.fullgenome.pggb.mapped.pack -t 4 yprp.fullgenome.pggb.giraffe.gbz > yprp.fullgenome.pggb.graph_calls.vcf\n",
+    "</details>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -254,6 +268,12 @@
   }
  ],
  "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
   "kernelspec": {
    "display_name": "nigms-pangenomics",
    "language": "python",