added stats on the vcf file

module_notebooks/05-variant-calling-with-vg.ipynb

@@ -225,6 +225,34 @@
     "!vg call SK1xyprp.chrVIII.pggb.aug.xg -k SK1xyprp.chrVIII.pggb.mapped.aug.pack -t 4 > SK1xyprp.chrVIII.pggb.aug_calls.vcf"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Generate stats on this VCF file. We will use `grep` to pull out the rows that start with SN."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!bcftools stats SK1xyprp.chrVIII.pggb.aug_calls.vcf | grep \"^SN\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "SNPs = single nucleotide polymorphisms (a single nucleotide change; reference and alternate alleles are all of length 1)  \n",
+    "MNPs = multi-nucleotide polymorphisms (reference and alternate alleles are all of the same length and that length is >1)  \n",
+    "indels = insertion/deletion (reference and alternate alleles are of different lengths)\n",
+    "others = more complex variants\n",
+    "multiallelic sites = more than one alternate allele\n",
+    "multiallelic SNP sites = more than one alternate allele at a SNP site"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -238,6 +266,7 @@
     "        <li>+ Create an index (xg).</li>\n",
     "        <li>+ Compute read support.</li>\n",
     "        <li>+ Generate a VCF.</li>\n",
+    "        <li>+ Generate statistics.</li>\n",
     "    </ul>"
    ]
   },
@@ -259,6 +288,7 @@
     "\n",
     "!vg call SK1xyprp.fullgenome.pggb.aug.xg -k SK1xyprp.fullgenome.pggb.mapped.aug.pack -t 4 > SK2xyprp.fullgenome.pggb.aug_calls.vcf\n",
     "\n",
+    "!bcftools stats SK1xyprp.fullgenome.pggb.aug_calls.vcf | grep \"^SN\"\n",
     "\n",
     "</details>"
    ]
@@ -282,6 +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",