02-simplify_vcf_samples.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from __future__ import annotations\n",
    "from io import BytesIO\n",
    "\n",
    "import numpy as np\n",
    "import oxbow as ox\n",
    "import pandas as pd\n",
    "import polars as pl\n",
    "import pyarrow as pa\n",
    "import pysam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [],
   "source": [
    "# This dictionary maps the VCF-derived input types to numpy/pandas dtypes\n",
    "TYPE_MAP = {\n",
    "    \"Integer\": \"int64\",\n",
    "    \"Float\": \"float64\",\n",
    "    \"String\": \"object\",\n",
    "    \"Flag\": \"bool\",\n",
    "}\n",
    "\n",
    "\n",
    "def read_vcf_as_pandas(vcf_path: str) -> pd.DataFrame:\n",
    "    ipc = ox.read_vcf(vcf_path)\n",
    "    return pa.ipc.open_file(BytesIO(ipc)).read_pandas()\n",
    "\n",
    "\n",
    "def read_vcf_as_polars(vcf_path: str) -> pl.DataFrame:\n",
    "    ipc = ox.read_vcf(vcf_path)\n",
    "    return pl.read_ipc(ipc)\n",
    "\n",
    "\n",
    "def read_info_schema(vcf_path: str) -> pd.DataFrame:\n",
    "    \"\"\" \n",
    "    Read the schema of the INFO column of a VCF.\n",
    "\n",
    "    This currently uses pysam.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "    vcf_path : str\n",
    "        Path to bgzipped vcf, with tabix indexed .tbi file with similar name \n",
    "        in same folder.\n",
    "    \n",
    "    Returns\n",
    "    -------\n",
    "    pd.DataFrame\n",
    "        Dataframe with [name, number, type] columns\n",
    "\n",
    "    Notes\n",
    "    -----\n",
    "    Possible values for `type` are: \"Integer\", \"Float\", \"String\", \"Flag\".\n",
    "\n",
    "    Possible values for `number` are:\n",
    "        - An integer (e.g. 0, 1, 2, 3, 4, etc.) - for fields where the number\n",
    "          of values per VCF record is fixed. 0 means the field is a \"Flag\".\n",
    "        - A string (\"A\", \"G\", \"R\") - for fields where the number of\n",
    "          values per VCF record is determined by the number of alts, the total\n",
    "          number of alleles, or the number of genotypes, respectively.\n",
    "        - A dot (\".\") - for fields where the number of values per VCF record\n",
    "          varies, is unknown, or is unbounded.\n",
    "    \"\"\"\n",
    "    with pysam.VariantFile(vcf_path) as f:\n",
    "        return pd.DataFrame(\n",
    "            [(obj.name, obj.number, obj.type, obj.description) for obj in f.header.info.values()],\n",
    "            columns=[\"name\", \"number\", \"type\", \"description\"],\n",
    "        )\n",
    "\n",
    "\n",
    "def read_format_schema(vcf_path: str) -> pd.DataFrame:\n",
    "    \"\"\" \n",
    "    Read the schema of the sample genotypes of a VCF.\n",
    "\n",
    "    This currently uses pysam.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "    vcf_path : str\n",
    "        Path to bgzipped vcf, with tabix indexed .tbi file with similar name \n",
    "        in same folder.\n",
    "    \n",
    "    Returns\n",
    "    -------\n",
    "    pd.DataFrame\n",
    "        Dataframe with [name, number, type] columns\n",
    "\n",
    "    Notes\n",
    "    -----\n",
    "    Possible values for `type` are: \"Integer\", \"Float\", \"String\", \"Flag\".\n",
    "\n",
    "    Possible values for `number` are:\n",
    "        - An integer (e.g. 0, 1, 2, 3, 4, etc.) - for fields where the number\n",
    "          of values per VCF record is fixed. 0 means the field is a \"Flag\".\n",
    "        - A string (\"A\", \"G\", \"R\") - for fields where the number of\n",
    "          values per VCF record is determined by the number of alts, the total\n",
    "          number of alleles, or the number of genotypes, respectively.\n",
    "        - A dot (\".\") - for fields where the number of values per VCF record\n",
    "          varies, is unknown, or is unbounded.\n",
    "    \"\"\"\n",
    "    with pysam.VariantFile(vcf_path) as f:\n",
    "        return pd.DataFrame(\n",
    "            [(obj.name, obj.number, obj.type, obj.description) for obj in f.header.formats.values()],\n",
    "            columns=[\"name\", \"number\", \"type\", \"description\"],\n",
    "        )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 142,
   "metadata": {},
   "outputs": [],
   "source": [
    "def read_vcf_as_pandas(\n",
    "    path: str,\n",
    "    query: tuple | None = None,\n",
    "    info_fields: list[str] | None = None,\n",
    "    sample_fields: list[str] | None = None,\n",
    "    samples: list[str] | None = None,\n",
    ") -> pd.DataFrame:\n",
    "    \n",
    "    f = pysam.VariantFile(path)\n",
    "    info_schema = read_info_schema(path)\n",
    "    sample_schema = read_format_schema(path)\n",
    "    info_arity = info_schema.set_index(\"name\")[\"number\"]\n",
    "    sample_arity = sample_schema.set_index(\"name\")[\"number\"]\n",
    "\n",
    "    if info_fields is None:\n",
    "        info_fields = list(info_schema[\"name\"])\n",
    "    if sample_fields is None:\n",
    "        sample_fields = list(sample_schema[\"name\"])\n",
    "    if samples is None:\n",
    "        samples = list(f.header.samples)\n",
    "    \n",
    "    if query is None:\n",
    "        record_iter = f\n",
    "    else:\n",
    "        record_iter = f.fetch(*query)\n",
    "\n",
    "    record_dicts = []\n",
    "    for record in record_iter:\n",
    "        record_dict = {\n",
    "            \"chrom\": record.chrom,\n",
    "            \"pos\": record.pos,\n",
    "            \"id\": record.id,\n",
    "            \"ref\": record.ref,\n",
    "            \"alts\": np.array(record.alts),\n",
    "            \"qual\": record.qual,\n",
    "            \"filters\": np.array(record.filter.keys()),\n",
    "        }\n",
    "        \n",
    "        for field in info_fields:\n",
    "            if field in record.info:\n",
    "                record_dict[field] = record.info[field]\n",
    "                if info_arity[field] not in {0, 1}:\n",
    "                    record_dict[field] = np.array(record_dict[field])\n",
    "            \n",
    "        for sample in samples:\n",
    "            for field in sample_fields:\n",
    "                if field in record.samples[sample]:\n",
    "                    record_dict[f\"{sample}.{field}\"] = record.samples[sample][field]\n",
    "                    if sample_arity[field] not in {0, 1}:\n",
    "                        record_dict[f\"{sample}.{field}\"] = np.array(record_dict[f\"{sample}.{field}\"])\n",
    "                if field == \"GT\":\n",
    "                    record_dict[f\"{sample}.{field}\"] = np.array(record_dict[f\"{sample}.{field}\"])\n",
    "                    record_dict[f\"{sample}.phased\"] = record.samples[sample].phased\n",
    "        record_dicts.append(record_dict)\n",
    "\n",
    "    df = pd.DataFrame.from_records(record_dicts)\n",
    "\n",
    "    columns = (\n",
    "        [\"chrom\", \"pos\", \"id\", \"ref\", \"alts\", \"qual\", \"filters\"] \n",
    "        + info_fields \n",
    "        + [f\"{sample}.{field}\" for sample in samples \n",
    "           for field in [*sample_fields, f\"phased\"]]\n",
    "    )\n",
    "\n",
    "    for col in columns:\n",
    "        if col not in df.columns:\n",
    "            df[col] = pd.NA\n",
    "\n",
    "    return df[columns].fillna(np.nan)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = read_vcf_as_pandas(\"DRR259112.ref.snpeff.vcf\", info_fields=[\"DP\"], sample_fields=[\"GT\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Find the longest alt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 143,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "chrom                  NC_045512.2\n",
       "pos                          21897\n",
       "id                            <NA>\n",
       "ref                              C\n",
       "alts                CTATATTAGAGTAG\n",
       "qual                   6963.600098\n",
       "filters                     [PASS]\n",
       "DP                             552\n",
       "DRR259112.GT                [0, 1]\n",
       "DRR259112.phased             False\n",
       "Name: 27, dtype: object"
      ]
     },
     "execution_count": 143,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2 = df.explode(\"alts\")\n",
    "df2.loc[df2['alts'].apply(len).idxmax()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 158,
   "metadata": {},
   "outputs": [],
   "source": [
    "info_fields = [\"LOF\"]\n",
    "df1 = read_vcf_as_pandas(\"DRR259112.ref.snpeff.vcf\", info_fields=info_fields, sample_fields=[\"GT\"])\n",
    "df2 = read_vcf_as_pandas(\"DRR259113.ref.snpeff.vcf.gz\", info_fields=info_fields, sample_fields=[\"GT\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 165,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>name</th>\n",
       "      <th>number</th>\n",
       "      <th>type</th>\n",
       "      <th>description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DP</td>\n",
       "      <td>1</td>\n",
       "      <td>Integer</td>\n",
       "      <td>Approximate read depth; some reads may have be...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AC</td>\n",
       "      <td>A</td>\n",
       "      <td>Integer</td>\n",
       "      <td>Allele count in genotypes, for each ALT allele...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AF</td>\n",
       "      <td>A</td>\n",
       "      <td>Float</td>\n",
       "      <td>Allele Frequency, for each ALT allele, in the ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AN</td>\n",
       "      <td>1</td>\n",
       "      <td>Integer</td>\n",
       "      <td>Total number of alleles in called genotypes</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>BaseQRankSum</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Z-score from Wilcoxon rank sum test of Alt Vs....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ExcessHet</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Phred-scaled p-value for exact test of excess ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>FS</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Phred-scaled p-value using Fisher's exact test...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>InbreedingCoeff</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Inbreeding coefficient as estimated from the g...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>MLEAC</td>\n",
       "      <td>A</td>\n",
       "      <td>Integer</td>\n",
       "      <td>Maximum likelihood expectation (MLE) for the a...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>MLEAF</td>\n",
       "      <td>A</td>\n",
       "      <td>Float</td>\n",
       "      <td>Maximum likelihood expectation (MLE) for the a...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>MQ</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>RMS Mapping Quality</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>MQRankSum</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Z-score From Wilcoxon rank sum test of Alt vs....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>QD</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Variant Confidence/Quality by Depth</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>RAW_MQandDP</td>\n",
       "      <td>2</td>\n",
       "      <td>Integer</td>\n",
       "      <td>Raw data (sum of squared MQ and total depth) f...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ReadPosRankSum</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Z-score from Wilcoxon rank sum test of Alt vs....</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>SOR</td>\n",
       "      <td>1</td>\n",
       "      <td>Float</td>\n",
       "      <td>Symmetric Odds Ratio of 2x2 contingency table ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>EFF</td>\n",
       "      <td>.</td>\n",
       "      <td>String</td>\n",
       "      <td>Predicted effects for this variant.Format: 'Ef...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>LOF</td>\n",
       "      <td>.</td>\n",
       "      <td>String</td>\n",
       "      <td>Predicted loss of function effects for this va...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>NMD</td>\n",
       "      <td>.</td>\n",
       "      <td>String</td>\n",
       "      <td>Predicted nonsense mediated decay effects for ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               name number     type  \\\n",
       "0                DP      1  Integer   \n",
       "1                AC      A  Integer   \n",
       "2                AF      A    Float   \n",
       "3                AN      1  Integer   \n",
       "4      BaseQRankSum      1    Float   \n",
       "5         ExcessHet      1    Float   \n",
       "6                FS      1    Float   \n",
       "7   InbreedingCoeff      1    Float   \n",
       "8             MLEAC      A  Integer   \n",
       "9             MLEAF      A    Float   \n",
       "10               MQ      1    Float   \n",
       "11        MQRankSum      1    Float   \n",
       "12               QD      1    Float   \n",
       "13      RAW_MQandDP      2  Integer   \n",
       "14   ReadPosRankSum      1    Float   \n",
       "15              SOR      1    Float   \n",
       "16              EFF      .   String   \n",
       "17              LOF      .   String   \n",
       "18              NMD      .   String   \n",
       "\n",
       "                                          description  \n",
       "0   Approximate read depth; some reads may have be...  \n",
       "1   Allele count in genotypes, for each ALT allele...  \n",
       "2   Allele Frequency, for each ALT allele, in the ...  \n",
       "3         Total number of alleles in called genotypes  \n",
       "4   Z-score from Wilcoxon rank sum test of Alt Vs....  \n",
       "5   Phred-scaled p-value for exact test of excess ...  \n",
       "6   Phred-scaled p-value using Fisher's exact test...  \n",
       "7   Inbreeding coefficient as estimated from the g...  \n",
       "8   Maximum likelihood expectation (MLE) for the a...  \n",
       "9   Maximum likelihood expectation (MLE) for the a...  \n",
       "10                                RMS Mapping Quality  \n",
       "11  Z-score From Wilcoxon rank sum test of Alt vs....  \n",
       "12                Variant Confidence/Quality by Depth  \n",
       "13  Raw data (sum of squared MQ and total depth) f...  \n",
       "14  Z-score from Wilcoxon rank sum test of Alt vs....  \n",
       "15  Symmetric Odds Ratio of 2x2 contingency table ...  \n",
       "16  Predicted effects for this variant.Format: 'Ef...  \n",
       "17  Predicted loss of function effects for this va...  \n",
       "18  Predicted nonsense mediated decay effects for ...  "
      ]
     },
     "execution_count": 165,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "read_info_schema(\"s3://sra-pub-sars-cov2/vcf/DRR259112/DRR259112.ref.snpeff.vcf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Merge VCFs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 161,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>chrom</th>\n",
       "      <th>pos</th>\n",
       "      <th>ref</th>\n",
       "      <th>LOF.DRR259112</th>\n",
       "      <th>DRR259112.GT</th>\n",
       "      <th>DRR259112.phased</th>\n",
       "      <th>LOF.DRR259113</th>\n",
       "      <th>DRR259113.GT</th>\n",
       "      <th>DRR259113.phased</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>241</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>316</td>\n",
       "      <td>TTT</td>\n",
       "      <td>[(leader|leader-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>2662</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>3371</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>4290</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>4456</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>4890</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>5497</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>6522</td>\n",
       "      <td>T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>6941</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>7927</td>\n",
       "      <td>AAAA</td>\n",
       "      <td>[(nsp3|nsp3-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>8782</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>10047</td>\n",
       "      <td>TTT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>10954</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>11103</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>12334</td>\n",
       "      <td>AAAA</td>\n",
       "      <td>[(nsp8|nsp8-gene|1|1.00)]</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>12494</td>\n",
       "      <td>TATA</td>\n",
       "      <td>[(nsp8|nsp8-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>13548</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>13732</td>\n",
       "      <td>AAA</td>\n",
       "      <td>[(RNA-dependent_RNA_polymerase-gene|RNA-depend...</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>15473</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>16596</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>18555</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>18755</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>18804</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>21387</td>\n",
       "      <td>TTT</td>\n",
       "      <td>[(2'-O-ribose_methyltransferase|2'-O-ribose_me...</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>21795</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>21844</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>21897</td>\n",
       "      <td>C</td>\n",
       "      <td>[(S|gene-GU280_gp02|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>22269</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>23035</td>\n",
       "      <td>TT</td>\n",
       "      <td>[(S|gene-GU280_gp02|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>23334</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>25714</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>25827</td>\n",
       "      <td>TTTT</td>\n",
       "      <td>[(ORF3a|gene-GU280_gp03|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>26764</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>28144</td>\n",
       "      <td>T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>29095</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>797</td>\n",
       "      <td>AA</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>2114</td>\n",
       "      <td>T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>4185</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>4313</td>\n",
       "      <td>AAAA</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(nsp3|nsp3-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>6028</td>\n",
       "      <td>AAA</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(nsp3|nsp3-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>10161</td>\n",
       "      <td>TTT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(3C-like_proteinase-gene|3C-like_proteinase-g...</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>10562</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>11075</td>\n",
       "      <td>TTTTTT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(nsp6|nsp6-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>11096</td>\n",
       "      <td>TTTT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(nsp6|nsp6-gene|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>11942</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>16375</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>21886</td>\n",
       "      <td>T</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>23959</td>\n",
       "      <td>TTT</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(S|gene-GU280_gp02|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>24035</td>\n",
       "      <td>AAA</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[(S|gene-GU280_gp02|1|1.00)]</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>24374</td>\n",
       "      <td>C</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[0, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>NC_045512.2</td>\n",
       "      <td>29705</td>\n",
       "      <td>G</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>[1, 1]</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          chrom    pos     ref  \\\n",
       "0   NC_045512.2    241       C   \n",
       "1   NC_045512.2    316     TTT   \n",
       "2   NC_045512.2   2662       C   \n",
       "3   NC_045512.2   3371       G   \n",
       "4   NC_045512.2   4290       C   \n",
       "5   NC_045512.2   4456       C   \n",
       "6   NC_045512.2   4890       C   \n",
       "7   NC_045512.2   5497       C   \n",
       "8   NC_045512.2   6522       T   \n",
       "9   NC_045512.2   6941       C   \n",
       "10  NC_045512.2   7927    AAAA   \n",
       "11  NC_045512.2   8782       C   \n",
       "12  NC_045512.2  10047     TTT   \n",
       "13  NC_045512.2  10954       C   \n",
       "14  NC_045512.2  11103       C   \n",
       "15  NC_045512.2  12334    AAAA   \n",
       "16  NC_045512.2  12494    TATA   \n",
       "17  NC_045512.2  13548       C   \n",
       "18  NC_045512.2  13732     AAA   \n",
       "19  NC_045512.2  15473       G   \n",
       "20  NC_045512.2  16596       C   \n",
       "21  NC_045512.2  18555       C   \n",
       "22  NC_045512.2  18755       C   \n",
       "23  NC_045512.2  18804       C   \n",
       "24  NC_045512.2  21387     TTT   \n",
       "25  NC_045512.2  21795       G   \n",
       "26  NC_045512.2  21844       C   \n",
       "27  NC_045512.2  21897       C   \n",
       "28  NC_045512.2  22269       C   \n",
       "29  NC_045512.2  23035      TT   \n",
       "30  NC_045512.2  23334       C   \n",
       "31  NC_045512.2  25714       C   \n",
       "32  NC_045512.2  25827    TTTT   \n",
       "33  NC_045512.2  26764       C   \n",
       "34  NC_045512.2  28144       T   \n",
       "35  NC_045512.2  29095       C   \n",
       "36  NC_045512.2    797      AA   \n",
       "37  NC_045512.2   2114       T   \n",
       "38  NC_045512.2   4185       G   \n",
       "39  NC_045512.2   4313    AAAA   \n",
       "40  NC_045512.2   6028     AAA   \n",
       "41  NC_045512.2  10161     TTT   \n",
       "42  NC_045512.2  10562       G   \n",
       "43  NC_045512.2  11075  TTTTTT   \n",
       "44  NC_045512.2  11096    TTTT   \n",
       "45  NC_045512.2  11942       C   \n",
       "46  NC_045512.2  16375       C   \n",
       "47  NC_045512.2  21886       T   \n",
       "48  NC_045512.2  23959     TTT   \n",
       "49  NC_045512.2  24035     AAA   \n",
       "50  NC_045512.2  24374       C   \n",
       "51  NC_045512.2  29705       G   \n",
       "\n",
       "                                        LOF.DRR259112 DRR259112.GT  \\\n",
       "0                                                 NaN       [0, 1]   \n",
       "1                       [(leader|leader-gene|1|1.00)]       [0, 1]   \n",
       "2                                                 NaN       [1, 1]   \n",
       "3                                                 NaN       [0, 1]   \n",
       "4                                                 NaN       [0, 1]   \n",
       "5                                                 NaN       [1, 1]   \n",
       "6                                                 NaN       [0, 1]   \n",
       "7                                                 NaN       [0, 1]   \n",
       "8                                                 NaN       [0, 1]   \n",
       "9                                                 NaN       [0, 1]   \n",
       "10                          [(nsp3|nsp3-gene|1|1.00)]       [0, 1]   \n",
       "11                                                NaN       [0, 1]   \n",
       "12                                                NaN       [0, 1]   \n",
       "13                                                NaN       [0, 1]   \n",
       "14                                                NaN       [0, 1]   \n",
       "15                          [(nsp8|nsp8-gene|1|1.00)]       [1, 1]   \n",
       "16                          [(nsp8|nsp8-gene|1|1.00)]       [0, 1]   \n",
       "17                                                NaN       [1, 1]   \n",
       "18  [(RNA-dependent_RNA_polymerase-gene|RNA-depend...       [0, 1]   \n",
       "19                                                NaN       [0, 1]   \n",
       "20                                                NaN       [1, 1]   \n",
       "21                                                NaN       [0, 1]   \n",
       "22                                                NaN       [0, 1]   \n",
       "23                                                NaN       [0, 1]   \n",
       "24  [(2'-O-ribose_methyltransferase|2'-O-ribose_me...       [0, 1]   \n",
       "25                                                NaN       [0, 1]   \n",
       "26                                                NaN       [0, 1]   \n",
       "27                       [(S|gene-GU280_gp02|1|1.00)]       [0, 1]   \n",
       "28                                                NaN       [0, 1]   \n",
       "29                       [(S|gene-GU280_gp02|1|1.00)]       [0, 1]   \n",
       "30                                                NaN       [0, 1]   \n",
       "31                                                NaN       [0, 1]   \n",
       "32                   [(ORF3a|gene-GU280_gp03|1|1.00)]       [0, 1]   \n",
       "33                                                NaN       [0, 1]   \n",
       "34                                                NaN       [0, 1]   \n",
       "35                                                NaN       [0, 1]   \n",
       "36                                                NaN          NaN   \n",
       "37                                                NaN          NaN   \n",
       "38                                                NaN          NaN   \n",
       "39                                                NaN          NaN   \n",
       "40                                                NaN          NaN   \n",
       "41                                                NaN          NaN   \n",
       "42                                                NaN          NaN   \n",
       "43                                                NaN          NaN   \n",
       "44                                                NaN          NaN   \n",
       "45                                                NaN          NaN   \n",
       "46                                                NaN          NaN   \n",
       "47                                                NaN          NaN   \n",
       "48                                                NaN          NaN   \n",
       "49                                                NaN          NaN   \n",
       "50                                                NaN          NaN   \n",
       "51                                                NaN          NaN   \n",
       "\n",
       "   DRR259112.phased                                      LOF.DRR259113  \\\n",
       "0             False                                                NaN   \n",
       "1             False                                                NaN   \n",
       "2             False                                                NaN   \n",
       "3             False                                                NaN   \n",
       "4             False                                                NaN   \n",
       "5             False                                                NaN   \n",
       "6             False                                                NaN   \n",
       "7             False                                                NaN   \n",
       "8             False                                                NaN   \n",
       "9             False                                                NaN   \n",
       "10            False                                                NaN   \n",
       "11            False                                                NaN   \n",
       "12            False                                                NaN   \n",
       "13            False                                                NaN   \n",
       "14            False                                                NaN   \n",
       "15            False                                                NaN   \n",
       "16            False                                                NaN   \n",
       "17            False                                                NaN   \n",
       "18            False                                                NaN   \n",
       "19            False                                                NaN   \n",
       "20            False                                                NaN   \n",
       "21            False                                                NaN   \n",
       "22            False                                                NaN   \n",
       "23            False                                                NaN   \n",
       "24            False                                                NaN   \n",
       "25            False                                                NaN   \n",
       "26            False                                                NaN   \n",
       "27            False                                                NaN   \n",
       "28            False                                                NaN   \n",
       "29            False                                                NaN   \n",
       "30            False                                                NaN   \n",
       "31            False                                                NaN   \n",
       "32            False                                                NaN   \n",
       "33            False                                                NaN   \n",
       "34            False                                                NaN   \n",
       "35            False                                                NaN   \n",
       "36              NaN                                                NaN   \n",
       "37              NaN                                                NaN   \n",
       "38              NaN                                                NaN   \n",
       "39              NaN                          [(nsp3|nsp3-gene|1|1.00)]   \n",
       "40              NaN                          [(nsp3|nsp3-gene|1|1.00)]   \n",
       "41              NaN  [(3C-like_proteinase-gene|3C-like_proteinase-g...   \n",
       "42              NaN                                                NaN   \n",
       "43              NaN                          [(nsp6|nsp6-gene|1|1.00)]   \n",
       "44              NaN                          [(nsp6|nsp6-gene|1|1.00)]   \n",
       "45              NaN                                                NaN   \n",
       "46              NaN                                                NaN   \n",
       "47              NaN                                                NaN   \n",
       "48              NaN                       [(S|gene-GU280_gp02|1|1.00)]   \n",
       "49              NaN                       [(S|gene-GU280_gp02|1|1.00)]   \n",
       "50              NaN                                                NaN   \n",
       "51              NaN                                                NaN   \n",
       "\n",
       "   DRR259113.GT DRR259113.phased  \n",
       "0           NaN              NaN  \n",
       "1           NaN              NaN  \n",
       "2        [1, 1]            False  \n",
       "3           NaN              NaN  \n",
       "4           NaN              NaN  \n",
       "5           NaN              NaN  \n",
       "6           NaN              NaN  \n",
       "7           NaN              NaN  \n",
       "8           NaN              NaN  \n",
       "9           NaN              NaN  \n",
       "10          NaN              NaN  \n",
       "11       [1, 1]            False  \n",
       "12          NaN              NaN  \n",
       "13          NaN              NaN  \n",
       "14          NaN              NaN  \n",
       "15          NaN              NaN  \n",
       "16          NaN              NaN  \n",
       "17          NaN              NaN  \n",
       "18          NaN              NaN  \n",
       "19          NaN              NaN  \n",
       "20          NaN              NaN  \n",
       "21          NaN              NaN  \n",
       "22          NaN              NaN  \n",
       "23          NaN              NaN  \n",
       "24          NaN              NaN  \n",
       "25          NaN              NaN  \n",
       "26          NaN              NaN  \n",
       "27          NaN              NaN  \n",
       "28          NaN              NaN  \n",
       "29          NaN              NaN  \n",
       "30          NaN              NaN  \n",
       "31          NaN              NaN  \n",
       "32          NaN              NaN  \n",
       "33          NaN              NaN  \n",
       "34       [1, 1]            False  \n",
       "35       [1, 1]            False  \n",
       "36       [0, 1]            False  \n",
       "37       [0, 1]            False  \n",
       "38       [0, 1]            False  \n",
       "39       [0, 1]            False  \n",
       "40       [0, 1]            False  \n",
       "41       [0, 1]            False  \n",
       "42       [0, 1]            False  \n",
       "43       [0, 1]            False  \n",
       "44       [0, 1]            False  \n",
       "45       [0, 1]            False  \n",
       "46       [0, 1]            False  \n",
       "47       [1, 1]            False  \n",
       "48       [0, 1]            False  \n",
       "49       [0, 1]            False  \n",
       "50       [0, 1]            False  \n",
       "51       [1, 1]            False  "
      ]
     },
     "execution_count": 161,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.merge(\n",
    "    df1.drop(columns=[\"qual\", \"id\", \"alts\", \"filters\"]),\n",
    "    df2.drop(columns=[\"qual\", \"id\", \"alts\", \"filters\"]),\n",
    "    how=\"outer\",\n",
    "    on=[\"chrom\", \"pos\", \"ref\"],\n",
    "    suffixes=(\".DRR259112\", \".DRR259113\")\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def to_parquet(ddf, outpath, compression=\"snappy\", row_group_size=100000, **kwargs):\n",
    "    try:\n",
    "        for i, partition in enumerate(ddf.partitions):\n",
    "            df = partition.compute()\n",
    "            table = pa.Table.from_pandas(df, preserve_index=False)\n",
    "            if i == 0:\n",
    "                writer = pa.parquet.ParquetWriter(\n",
    "                    outpath,\n",
    "                    table.schema,\n",
    "                    compression=compression,\n",
    "                    **kwargs\n",
    "                )\n",
    "            writer.write_table(table, row_group_size=row_group_size)\n",
    "    finally:\n",
    "        writer.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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