Fixed typos and filename.

ncgr · Feb 10, 2025 · 2118add · 2118add
1 parent 2aff2df
commit 2118add
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/module_notebooks/05-variant-calling-with-vg.ipynb b/module_notebooks/05-variant-calling-with-vg.ipynb
@@ -100,7 +100,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!vg call -k yprp.chrVIII.pggb.mapped.pack -t 4 yprp.chrVIII.pggb.giraffe.gbz > yprp.chrVIII.pggb.graph_calls.vcf"
+    "!vg call -k yprp.chrVIII.pggb.mapped.pack -t 4 yprp.chrVIII.pggb.giraffe.gbz > SK1xyprp.chrVIII.pggb.graph_calls.vcf"
    ]
   },
   {
@@ -286,7 +286,7 @@
     "\n",
     "!vg pack -x SK1xyprp.fullgenome.pggb.aug.xg -g SK1xyprp.fullgenome.pggb.mapped.aug.gam -Q 5 -s 5 -o SK1xyprp.fullgenome.pggb.mapped.aug.pack -t 4\n",
     "\n",
-    "!vg call SK1xyprp.fullgenome.pggb.aug.xg -k SK1xyprp.fullgenome.pggb.mapped.aug.pack -t 4 > SK2xyprp.fullgenome.pggb.aug_calls.vcf\n",
+    "!vg call SK1xyprp.fullgenome.pggb.aug.xg -k SK1xyprp.fullgenome.pggb.mapped.aug.pack -t 4 > SK1xyprp.fullgenome.pggb.aug_calls.vcf\n",
     "\n",
     "!bcftools stats SK1xyprp.fullgenome.pggb.aug_calls.vcf | grep \"^SN\"\n",
     "\n",
@@ -312,6 +312,12 @@
   }
  ],
  "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",