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Github Action: Lint Notebooks
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‎module_notebooks/07-variant-calling-with-vg.ipynb‎

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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"mkdir: cannot create directory ‘variants’: File exists\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!mkdir variants"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"[vg call]: You can restrict the search to GBZ haplotypes, often to the benefict of speed and accuracy, with the -z option\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!vg call -k alignments/yprp.chrVIII.pggb.mapped.pack -t 4 graphs/yprp.chrVIII.pggb.giraffe.gbz > variants/SK1xyprp.chrVIII.pggb.graph_calls.vcf"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"SN\t0\tnumber of samples:\t1\n",
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"SN\t0\tnumber of records:\t4573\n",
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"SN\t0\tnumber of no-ALTs:\t0\n",
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"SN\t0\tnumber of SNPs:\t3997\n",
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"SN\t0\tnumber of MNPs:\t186\n",
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"SN\t0\tnumber of indels:\t358\n",
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"SN\t0\tnumber of others:\t41\n",
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"SN\t0\tnumber of multiallelic sites:\t32\n",
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"SN\t0\tnumber of multiallelic SNP sites:\t6\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!bcftools stats variants/SK1xyprp.chrVIII.pggb.graph_calls.vcf | grep \"^SN\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"\n",
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" <iframe\n",
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" width=\"800\"\n",
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" height=\"400\"\n",
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" src=\"../html/flashcard_variants.html\"\n",
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" frameborder=\"0\"\n",
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" allowfullscreen\n",
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" \n",
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" ></iframe>\n",
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" "
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],
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"text/plain": [
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"<IPython.lib.display.IFrame at 0x7f14893989b0>"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.display import IFrame\n",
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"IFrame('../html/flashcard_variants.html', width=800, height=400)"
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},
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{
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"cell_type": "code",
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},
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"cell_type": "code",
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},
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"cell_type": "code",
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"SN\t0\tnumber of samples:\t1\n",
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"SN\t0\tnumber of records:\t5401\n",
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"SN\t0\tnumber of no-ALTs:\t0\n",
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"SN\t0\tnumber of SNPs:\t4549\n",
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"SN\t0\tnumber of MNPs:\t495\n",
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"SN\t0\tnumber of indels:\t358\n",
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"SN\t0\tnumber of others:\t108\n",
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"SN\t0\tnumber of multiallelic sites:\t239\n",
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"SN\t0\tnumber of multiallelic SNP sites:\t56\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!bcftools stats variants/SK1xyprp.chrVIII.pggb.aug_calls.vcf | grep \"^SN\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"SN\t0\tnumber of samples:\t1\n",
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"SN\t0\tnumber of records:\t83627\n",
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"SN\t0\tnumber of no-ALTs:\t0\n",
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"SN\t0\tnumber of SNPs:\t73426\n",
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"SN\t0\tnumber of MNPs:\t3126\n",
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"SN\t0\tnumber of indels:\t6327\n",
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"SN\t0\tnumber of others:\t880\n",
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"SN\t0\tnumber of multiallelic sites:\t347\n",
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"SN\t0\tnumber of multiallelic SNP sites:\t27\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!vg convert graphs/yprp.fullgenome.pggb.giraffe.gbz > graphs/yprp.fullgenome.pggb.giraffe.vg\n",
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"\n",
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},
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{
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"cell_type": "code",
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},
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"cell_type": "code",
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},
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{
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"cell_type": "code",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"SN\t0\tnumber of samples:\t2\n",
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"SN\t0\tnumber of records:\t5979\n",
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"SN\t0\tnumber of no-ALTs:\t0\n",
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"SN\t0\tnumber of SNPs:\t5327\n",
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"SN\t0\tnumber of MNPs:\t220\n",
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"SN\t0\tnumber of indels:\t455\n",
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"SN\t0\tnumber of others:\t47\n",
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"SN\t0\tnumber of multiallelic sites:\t169\n",
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"SN\t0\tnumber of multiallelic SNP sites:\t35\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!bcftools stats variants/yprp.chrVIII.pggb.S288Cpaths.deconstruct.vcf | grep \"^SN\""
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]
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},
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{
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"cell_type": "code",
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},
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"cell_type": "code",
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"data": {
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"text/html": [
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"\n",
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" <iframe\n",
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" width=\"800\"\n",
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" height=\"400\"\n",
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" src=\"../html/flashcard_viz.html\"\n",
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" frameborder=\"0\"\n",
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" allowfullscreen\n",
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" \n",
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" ></iframe>\n",
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" "
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],
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"text/plain": [
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"<IPython.lib.display.IFrame at 0x7f7e8d3dc0e0>"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.display import IFrame\n",
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"IFrame('../html/flashcard_viz.html', width=800, height=400)"
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}
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],
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"metadata": {
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"environment": {
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"kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
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"name": "workbench-notebooks.m129",
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"type": "gcloud",
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"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
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},
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"kernelspec": {
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"display_name": "nigms-pangenomics (Local) (Local)",
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"language": "python",

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