genosecretor 0.1.0__tar.gz

genosecretor-0.1.0/.cache/.gitignore

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+*

genosecretor-0.1.0/.cache/1229514038324329839

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+{
+  "data": {
+    "meta": {},
+    "content": "<h1 id=\"inference-methods\">Inference methods<a class=\"headerlink\" href=\"#inference-methods\" title=\"Permanent link\">&para;</a></h1>\n<p>genoSecretor maps FUT2 tag SNPs to haplotype alleles <strong>Se</strong> (functional), <strong>se</strong> (complete LoF, se428 / W143X), and <strong>Se^w</strong> (reduced activity, se385 / I129F), then to a recessive phenotype.</p>\n<blockquote>\n<p><strong>Research use only.</strong> These methods type common alleles, not the full FUT2 allelic series. FUT3/Lewis typing is out of scope.</p>\n</blockquote>\n<h2 id=\"haplotype-rules\">Haplotype rules<a class=\"headerlink\" href=\"#haplotype-rules\" title=\"Permanent link\">&para;</a></h2>\n<p>For each chromosome copy:</p>\n<ol>\n<li>If rs601338 = <code>LOF</code> → haplotype = <strong>se</strong> (epistatic: truncated FUT2 is null even if rs1047781 is also <code>WEAK</code>)</li>\n<li>Else if rs1047781 = <code>WEAK</code> → haplotype = <strong>Se^w</strong></li>\n<li>Else if either marker is <code>FUNCTIONAL</code> → haplotype = <strong>Se</strong></li>\n<li>Else → haplotype = <strong>unknown</strong></li>\n</ol>\n<p><img alt=\"Per-haplotype FUT2 calling rules\" src=\"../assets/figures/secretor-haplotype-rules.svg\" width=\"100%\" /></p>\n<p><em>Figure. One chromosome copy: <code>LOF</code> yields </em><em>se</em><em>; otherwise <code>WEAK</code> yields </em><em>Se^w</em><em> and <code>FUNCTIONAL</code> yields </em><em>Se</em><em>. Under <code>proxy</code>, rs601338 / rs602662 copy-count disagreement is CONFLICT, not a forced haplotype.</em></p>\n<h2 id=\"phenotype-table\">Phenotype table<a class=\"headerlink\" href=\"#phenotype-table\" title=\"Permanent link\">&para;</a></h2>\n<table>\n<thead>\n<tr>\n<th>Diplotype</th>\n<th><code>secretor_status</code></th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>Se/Se, Se/se, Se/Se^w</td>\n<td>secretor</td>\n</tr>\n<tr>\n<td>Se^w/Se^w, Se^w/se</td>\n<td>weak-secretor</td>\n</tr>\n<tr>\n<td>se/se</td>\n<td>non-secretor</td>\n</tr>\n</tbody>\n</table>\n<p><code>--phenotype-coding biochemical</code> (default) uses this table. <code>--phenotype-coding gwas</code> recodes <code>Se^w/Se^w</code> and <code>Se^w/se</code> as <strong>non-secretor</strong> (Smyth 2011 / BBJ-style binary trait). <code>fut2_genotype</code> still keeps <code>Se^w</code>.</p>\n<table>\n<thead>\n<tr>\n<th>Diplotype</th>\n<th>biochemical</th>\n<th>gwas</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>Se/Se, Se/se, Se/Se^w</td>\n<td>secretor</td>\n<td>secretor</td>\n</tr>\n<tr>\n<td>Se^w/Se^w, Se^w/se</td>\n<td>weak-secretor</td>\n<td>non-secretor</td>\n</tr>\n<tr>\n<td>se/se</td>\n<td>non-secretor</td>\n<td>non-secretor</td>\n</tr>\n</tbody>\n</table>\n<p><img alt=\"Diplotype to secretor phenotype\" src=\"../assets/figures/secretor-diplotype-phenotype.svg\" width=\"100%\" /></p>\n<p><em>Figure. Sorted haplotypes (Se &lt; Se^w &lt; se) map to phenotype: any Se copy → secretor; Se^w/Se^w and Se^w/se → weak-secretor; se/se → non-secretor.</em></p>\n<h2 id=\"two-marker-default-when-both-snps-are-present\">two-marker (default when both SNPs are present)<a class=\"headerlink\" href=\"#two-marker-default-when-both-snps-are-present\" title=\"Permanent link\">&para;</a></h2>\n<p>Uses rs601338 and rs1047781.</p>\n<p>Unphased double heterozygotes (het at both SNPs) are assigned <strong>Se^w/se</strong> under <code>--assume-trans</code> (default), because se428 and se385 typically sit on different continental haplotypes. <code>--no-assume-trans</code> leaves those samples ambiguous (<code>Se^w/se</code> vs cis <code>Se/se</code>).</p>\n<p><img alt=\"Unphased double heterozygote is Se^w/se or Se/se\" src=\"../assets/figures/secretor-unphased-double-het.svg\" width=\"100%\" /></p>\n<p><em>Figure. Unphased <code>LOF</code>/<code>FUNCTIONAL</code> × <code>FUNCTIONAL</code>/<code>WEAK</code> is compatible with trans Se^w/se or cis Se/se (the double-mutant copy is still </em><em>se</em><em>). Default <code>--assume-trans</code> assigns </em><em>Se^w/se</em><em>; <code>--no-assume-trans</code> leaves the call ambiguous. Phased GT does not use this assumption.</em></p>\n<h2 id=\"common\">common<a class=\"headerlink\" href=\"#common\" title=\"Permanent link\">&para;</a></h2>\n<p>rs601338 only. Homozygous LOF → se/se (non-secretor); otherwise secretor. Never emits weak-secretor. Poor choice as the sole method in East Asian cohorts.</p>\n<h2 id=\"eas\">eas<a class=\"headerlink\" href=\"#eas\" title=\"Permanent link\">&para;</a></h2>\n<p>rs1047781 only. Homozygous WEAK → Se^w/Se^w (weak-secretor); otherwise secretor. Never emits se/se from W143X. Poor choice as the sole method in European/African cohorts.</p>\n<h2 id=\"proxy\">proxy<a class=\"headerlink\" href=\"#proxy\" title=\"Permanent link\">&para;</a></h2>\n<p>If rs601338 is usable, same as <code>common</code>. If it is missing, rs602662 SE_PROXY (A) is mapped to an LOF-like state and confidence is <strong>low</strong>. If both markers are present and copy counts disagree, QC status is CONFLICT.</p>\n<h2 id=\"auto-selection\">Auto-selection<a class=\"headerlink\" href=\"#auto-selection\" title=\"Permanent link\">&para;</a></h2>\n<ol>\n<li>two-marker if rs601338 and rs1047781 are present</li>\n<li>common if rs601338 is present</li>\n<li>eas if rs1047781 is present</li>\n<li>proxy if rs602662 is present (low confidence)</li>\n</ol>\n<p><code>--strict-method</code> disables fallback when a requested method's minimum markers are missing.</p>\n<p>List methods:</p>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-0-1\"><a id=\"__codelineno-0-1\" name=\"__codelineno-0-1\" href=\"#__codelineno-0-1\"></a>genosecretor<span class=\"w\"> </span>--methods\n</span><span id=\"__span-0-2\"><a id=\"__codelineno-0-2\" name=\"__codelineno-0-2\" href=\"#__codelineno-0-2\"></a>genosecretor<span class=\"w\"> </span>--method-info<span class=\"w\"> </span>two-marker\n</span></code></pre></div>",
+    "search": [
+      {
+        "location": null,
+        "level": 1,
+        "title": "Inference methods",
+        "text": "<p>genoSecretor maps FUT2 tag SNPs to haplotype alleles Se (functional), se (complete LoF, se428 / W143X), and Se^w (reduced activity, se385 / I129F), then to a recessive phenotype.</p> <p>Research use only. These methods type common alleles, not the full FUT2 allelic series. FUT3/Lewis typing is out of scope.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "haplotype-rules",
+        "level": 2,
+        "title": "Haplotype rules",
+        "text": "<p>For each chromosome copy:</p> <ol> <li>If rs601338 = <code>LOF</code> → haplotype = se (epistatic: truncated FUT2 is null even if rs1047781 is also <code>WEAK</code>)</li> <li>Else if rs1047781 = <code>WEAK</code> → haplotype = Se^w</li> <li>Else if either marker is <code>FUNCTIONAL</code> → haplotype = Se</li> <li>Else → haplotype = unknown</li> </ol> <p></p> <p>Figure. One chromosome copy: <code>LOF</code> yields se; otherwise <code>WEAK</code> yields Se^w and <code>FUNCTIONAL</code> yields Se. Under <code>proxy</code>, rs601338 / rs602662 copy-count disagreement is CONFLICT, not a forced haplotype.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "phenotype-table",
+        "level": 2,
+        "title": "Phenotype table",
+        "text": "Diplotype <code>secretor_status</code> Se/Se, Se/se, Se/Se^w secretor Se^w/Se^w, Se^w/se weak-secretor se/se non-secretor <p><code>--phenotype-coding biochemical</code> (default) uses this table. <code>--phenotype-coding gwas</code> recodes <code>Se^w/Se^w</code> and <code>Se^w/se</code> as non-secretor (Smyth 2011 / BBJ-style binary trait). <code>fut2_genotype</code> still keeps <code>Se^w</code>.</p> Diplotype biochemical gwas Se/Se, Se/se, Se/Se^w secretor secretor Se^w/Se^w, Se^w/se weak-secretor non-secretor se/se non-secretor non-secretor <p></p> <p>Figure. Sorted haplotypes (Se &lt; Se^w &lt; se) map to phenotype: any Se copy → secretor; Se^w/Se^w and Se^w/se → weak-secretor; se/se → non-secretor.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "two-marker-default-when-both-snps-are-present",
+        "level": 2,
+        "title": "two-marker (default when both SNPs are present)",
+        "text": "<p>Uses rs601338 and rs1047781.</p> <p>Unphased double heterozygotes (het at both SNPs) are assigned Se^w/se under <code>--assume-trans</code> (default), because se428 and se385 typically sit on different continental haplotypes. <code>--no-assume-trans</code> leaves those samples ambiguous (<code>Se^w/se</code> vs cis <code>Se/se</code>).</p> <p></p> <p>Figure. Unphased <code>LOF</code>/<code>FUNCTIONAL</code> × <code>FUNCTIONAL</code>/<code>WEAK</code> is compatible with trans Se^w/se or cis Se/se (the double-mutant copy is still se). Default <code>--assume-trans</code> assigns Se^w/se; <code>--no-assume-trans</code> leaves the call ambiguous. Phased GT does not use this assumption.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "common",
+        "level": 2,
+        "title": "common",
+        "text": "<p>rs601338 only. Homozygous LOF → se/se (non-secretor); otherwise secretor. Never emits weak-secretor. Poor choice as the sole method in East Asian cohorts.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "eas",
+        "level": 2,
+        "title": "eas",
+        "text": "<p>rs1047781 only. Homozygous WEAK → Se^w/Se^w (weak-secretor); otherwise secretor. Never emits se/se from W143X. Poor choice as the sole method in European/African cohorts.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "proxy",
+        "level": 2,
+        "title": "proxy",
+        "text": "<p>If rs601338 is usable, same as <code>common</code>. If it is missing, rs602662 SE_PROXY (A) is mapped to an LOF-like state and confidence is low. If both markers are present and copy counts disagree, QC status is CONFLICT.</p>",
+        "path": [],
+        "tags": []
+      },
+      {
+        "location": "auto-selection",
+        "level": 2,
+        "title": "Auto-selection",
+        "text": "<ol> <li>two-marker if rs601338 and rs1047781 are present</li> <li>common if rs601338 is present</li> <li>eas if rs1047781 is present</li> <li>proxy if rs602662 is present (low confidence)</li> </ol> <p><code>--strict-method</code> disables fallback when a requested method's minimum markers are missing.</p> <p>List methods:</p> <pre><code>genosecretor --methods\ngenosecretor --method-info two-marker\n</code></pre>",
+        "path": [],
+        "tags": []
+      }
+    ],
+    "title": "Inference methods",
+    "toc": [
+      {
+        "title": "Inference methods",
+        "id": "inference-methods",
+        "url": "#inference-methods",
+        "children": [
+          {
+            "title": "Haplotype rules",
+            "id": "haplotype-rules",
+            "url": "#haplotype-rules",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "Phenotype table",
+            "id": "phenotype-table",
+            "url": "#phenotype-table",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "two-marker (default when both SNPs are present)",
+            "id": "two-marker-default-when-both-snps-are-present",
+            "url": "#two-marker-default-when-both-snps-are-present",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "common",
+            "id": "common",
+            "url": "#common",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "eas",
+            "id": "eas",
+            "url": "#eas",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "proxy",
+            "id": "proxy",
+            "url": "#proxy",
+            "children": [],
+            "level": 2
+          },
+          {
+            "title": "Auto-selection",
+            "id": "auto-selection",
+            "url": "#auto-selection",
+            "children": [],
+            "level": 2
+          }
+        ],
+        "level": 1
+      }
+    ]
+  },
+  "hash": 10971299751445454698
+}

genosecretor-0.1.0/.cache/12783978247058528628

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aria-label=\"On this page\">\n  \n  \n  \n    \n  \n  \n    <label class=\"md-nav__title\" for=\"__toc\">\n      <span class=\"md-nav__icon md-icon\"></span>\n      On this page\n    </label>\n    <ul class=\"md-nav__list\" data-md-component=\"toc\" data-md-scrollfix>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#what-is-modelled\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        What is modelled\n      \n    </span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#what-is-not-modelled\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        What is not modelled\n      \n    </span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#weak-secretor-vs-gwas-binary-coding\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        Weak-secretor vs GWAS binary coding\n      \n    </span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#-assume-trans\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        --assume-trans\n      \n    </span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#proxy-ld\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        Proxy LD\n      \n    </span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#validation\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        Validation\n      \n    </span>\n  </a>\n  \n</li>\n      \n    </ul>\n  \n</nav>\n                  </div>\n                </div>\n              </div>\n            \n          \n          \n            <div class=\"md-content\" data-md-component=\"content\">\n              \n              <article class=\"md-content__inner md-typeset\">\n                \n                  \n  \n  \n\n\n<h1 id=\"assumptions-and-limitations\">Assumptions and limitations<a class=\"headerlink\" href=\"#assumptions-and-limitations\" title=\"Permanent link\">&para;</a></h1>\n<blockquote>\n<p><strong>Research use only.</strong> genoSecretor infers FUT2 secretor status from a small set of tag SNPs. It is not a serological or clinical test.</p>\n</blockquote>\n<h2 id=\"what-is-modelled\">What is modelled<a class=\"headerlink\" href=\"#what-is-modelled\" title=\"Permanent link\">&para;</a></h2>\n<ul>\n<li>Recessive FUT2: two loss-of-function / weak haplotypes are required for non-secretor or weak-secretor phenotypes.</li>\n<li>se428 (rs601338 W143X) as a complete null.</li>\n<li>se385 (rs1047781 I129F) as a reduced-activity (weak) allele. Under default <code>--phenotype-coding biochemical</code>, homozygous or compound-with-se genotypes are <strong>weak-secretor</strong>. <code>--phenotype-coding gwas</code> recodes those calls as <strong>non-secretor</strong>.</li>\n<li>rs602662 as an LD proxy for se428 only.</li>\n</ul>\n<h2 id=\"what-is-not-modelled\">What is not modelled<a class=\"headerlink\" href=\"#what-is-not-modelled\" title=\"Permanent link\">&para;</a></h2>\n<ul>\n<li>Rare FUT2 nulls, fusions, and regulatory alleles.</li>\n<li>FUT3 / Lewis (Le^a / Le^b) phenotypes.</li>\n<li>Salivary ABH serology or norovirus binding assays.</li>\n<li>Calibrated probabilities (confidence is ordinal: high / medium / low / none).</li>\n</ul>\n<h2 id=\"weak-secretor-vs-gwas-binary-coding\">Weak-secretor vs GWAS binary coding<a class=\"headerlink\" href=\"#weak-secretor-vs-gwas-binary-coding\" title=\"Permanent link\">&para;</a></h2>\n<p>se385 is not a complete FUT2 null. Blood-group papers report residual enzyme activity and a <strong>weak-secretor</strong> / Le(a+b+) phenotype (Henry et al. 1996; Koda et al. 1996; Soejima and Koda 2021). Many GWAS papers treat homozygous se385 (rs1047781 T/T) as <strong>non-secretor</strong> (Smyth et al. 2011; He et al. 2023 BBJ peptic-ulcer coding).</p>\n<ul>\n<li><code>--phenotype-coding biochemical</code> (default): <code>Se^w/Se^w</code> and <code>Se^w/se</code> → <code>weak-secretor</code>; <code>se/se</code> → <code>non-secretor</code>.</li>\n<li><code>--phenotype-coding gwas</code>: those <code>Se^w</code> diplotypes are recoded as <code>non-secretor</code>. Heterozygotes with a functional Se copy (<code>Se/Se^w</code>, <code>Se/se</code>) stay secretor.</li>\n</ul>\n<p><code>fut2_genotype</code> always keeps <code>Se^w</code>. Python: <code>SecretorCaller(phenotype_coding=\"gwas\")</code>.</p>\n<h2 id=\"-assume-trans\"><code>--assume-trans</code><a class=\"headerlink\" href=\"#-assume-trans\" title=\"Permanent link\">&para;</a></h2>\n<p>Unphased heterozygotes at <strong>both</strong> functional SNPs are compatible with trans <code>Se^w/se</code> (weak-secretor) or cis <code>Se</code> plus a double-mutant haplotype (secretor). The default assigns trans. Pass <code>--no-assume-trans</code> to leave those samples ambiguous.</p>\n<p>In 1000 Genomes 30x hg38, that unphased pattern is rare because se428 and se385 almost never co-occur (zero double-hets in AFR/AMR/EUR; one trans double-het in EAS). See <a href=\"../examples/1kg-assume-trans/\">1000 Genomes <code>--assume-trans</code></a>. That check uses <strong>phase</strong>, not salivary serology.</p>\n<h2 id=\"proxy-ld\">Proxy LD<a class=\"headerlink\" href=\"#proxy-ld\" title=\"Permanent link\">&para;</a></h2>\n<p>rs602662 is strongly correlated with rs601338 in European cohorts and is a poorer tag in populations where se385 (not se428) is the common reduced-activity allele. Proxy calls are always low confidence.</p>\n<h2 id=\"validation\">Validation<a class=\"headerlink\" href=\"#validation\" title=\"Permanent link\">&para;</a></h2>\n<p>genoSecretor has not been validated against salivary ABH typing across ancestries.</p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n                \n              </article>\n            </div>\n          \n          \n  <script>var tabs=__md_get(\"__tabs\");if(Array.isArray(tabs))e:for(var set of document.querySelectorAll(\".tabbed-set\")){var labels=set.querySelector(\".tabbed-labels\");for(var tab of tabs)for(var label of labels.getElementsByTagName(\"label\"))if(label.innerText.trim()===tab){var input=document.getElementById(label.htmlFor);input.checked=!0;continue e}}</script>\n\n<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith(\"__tabbed_\"))</script>\n        </div>\n        \n          <button type=\"button\" class=\"md-top md-icon\" data-md-component=\"top\" hidden>\n  \n  <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-circle-arrow-up\" viewBox=\"0 0 24 24\"><circle cx=\"12\" cy=\"12\" r=\"10\"/><path d=\"m16 12-4-4-4 4M12 16V8\"/></svg>\n  Back to top\n</button>\n        \n      </main>\n      \n        <footer class=\"md-footer\">\n  \n    \n      \n      <nav class=\"md-footer__inner md-grid\" aria-label=\"Footer\" >\n        \n          \n          <a href=\"../markers/\" class=\"md-footer__link md-footer__link--prev\" aria-label=\"Previous: Markers\">\n            <div class=\"md-footer__button md-icon\">\n              \n              <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-arrow-left\" viewBox=\"0 0 24 24\"><path d=\"m12 19-7-7 7-7M19 12H5\"/></svg>\n            </div>\n            <div class=\"md-footer__title\">\n              <span class=\"md-footer__direction\">\n                Previous\n              </span>\n              <div class=\"md-ellipsis\">\n                Markers\n              </div>\n            </div>\n          </a>\n        \n        \n          \n          <a href=\"../examples/\" class=\"md-footer__link md-footer__link--next\" aria-label=\"Next: Examples\">\n            <div class=\"md-footer__title\">\n              <span class=\"md-footer__direction\">\n                Next\n              </span>\n              <div class=\"md-ellipsis\">\n                Examples\n              </div>\n            </div>\n            <div class=\"md-footer__button md-icon\">\n              \n              <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-arrow-right\" viewBox=\"0 0 24 24\"><path d=\"M5 12h14M12 5l7 7-7 7\"/></svg>\n            </div>\n          </a>\n        \n      </nav>\n    \n  \n  <div class=\"md-footer-meta md-typeset\">\n    <div class=\"md-footer-meta__inner md-grid\">\n      <div class=\"md-copyright\">\n  \n    <div class=\"md-copyright__highlight\">\n      Copyright &copy; 2026 Yunye He\n    </div>\n  \n  \n    Made with\n    <a href=\"https://zensical.org/\" target=\"_blank\" rel=\"noopener\">\n      Zensical\n    </a>\n  \n</div>\n      \n        \n<div class=\"md-social\">\n  \n    \n    \n    \n    \n      \n      \n    \n    <a href=\"https://github.com/cloufield/genoSecretor\" target=\"_blank\" rel=\"noopener\" title=\"github.com\" class=\"md-social__link\">\n      <svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 512 512\"><!--! 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genosecretor-0.1.0/.cache/12842651320362419197

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</span>\n  </a>\n  \n</li>\n      \n        <li class=\"md-nav__item\">\n  <a href=\"#see-also\" class=\"md-nav__link\">\n    <span class=\"md-ellipsis\">\n      \n        See also\n      \n    </span>\n  </a>\n  \n</li>\n      \n    </ul>\n  \n</nav>\n                  </div>\n                </div>\n              </div>\n            \n          \n          \n            <div class=\"md-content\" data-md-component=\"content\">\n              \n              <article class=\"md-content__inner md-typeset\">\n                \n                  \n  \n  \n\n\n<h1 id=\"usage\">Usage<a class=\"headerlink\" href=\"#usage\" title=\"Permanent link\">&para;</a></h1>\n<p>Install genoSecretor and infer FUT2 secretor status from a genotype file. For pipeline internals see <a href=\"../workflow/\">Workflow</a>; for haplotype rules see <a href=\"../methods/\">Inference methods</a>.</p>\n<div class=\"admonition warning\">\n<p class=\"admonition-title\">Research use only</p>\n<p>genoSecretor is intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research.\nGenotype-inferred secretor status does not capture all rare or atypical FUT2 alleles and\n<strong>must not</strong> be used for clinical decision-making.</p>\n</div>\n<h2 id=\"install\">Install<a class=\"headerlink\" href=\"#install\" title=\"Permanent link\">&para;</a></h2>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-0-1\"><a id=\"__codelineno-0-1\" name=\"__codelineno-0-1\" href=\"#__codelineno-0-1\"></a>pip<span class=\"w\"> </span>install<span class=\"w\"> </span>genosecretor\n</span></code></pre></div>\n<h2 id=\"quick-start\">Quick start<a class=\"headerlink\" href=\"#quick-start\" title=\"Permanent link\">&para;</a></h2>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-1-1\"><a id=\"__codelineno-1-1\" name=\"__codelineno-1-1\" href=\"#__codelineno-1-1\"></a>genosecretor<span class=\"w\"> </span>cohort.pgen<span class=\"w\"> </span>--out<span class=\"w\"> </span>secretor\n</span><span id=\"__span-1-2\"><a id=\"__codelineno-1-2\" name=\"__codelineno-1-2\" href=\"#__codelineno-1-2\"></a><span class=\"c1\"># writes: secretor.secretor.tsv, secretor.qc.tsv, secretor.summary.txt, secretor.report.html</span>\n</span></code></pre></div>\n<p>If <code>--out</code> is omitted, the prefix is the input path with its suffix stripped.</p>\n<h2 id=\"command-line-reference\">Command-line reference<a class=\"headerlink\" href=\"#command-line-reference\" title=\"Permanent link\">&para;</a></h2>\n<div class=\"language-text highlight\"><pre><span></span><code><span id=\"__span-2-1\"><a id=\"__codelineno-2-1\" name=\"__codelineno-2-1\" href=\"#__codelineno-2-1\"></a>genosecretor DATA [options]\n</span></code></pre></div>\n<table>\n<thead>\n<tr>\n<th>Flag</th>\n<th>Default</th>\n<th>Meaning</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td><code>DATA</code></td>\n<td>required</td>\n<td>Input genotype file</td>\n</tr>\n<tr>\n<td><code>-o</code> / <code>--out</code></td>\n<td>stem of <code>DATA</code></td>\n<td>Output prefix</td>\n</tr>\n<tr>\n<td><code>--format</code></td>\n<td><code>auto</code></td>\n<td><code>auto</code>, <code>vcf</code>, <code>bcf</code>, <code>bgen</code>, <code>pgen</code>, or <code>plink1</code></td>\n</tr>\n<tr>\n<td><code>--build</code></td>\n<td><code>auto</code></td>\n<td><code>auto</code>, <code>hg19</code>, <code>hg38</code>, or <code>chm13</code></td>\n</tr>\n<tr>\n<td><code>--method</code></td>\n<td><code>auto</code></td>\n<td><code>auto</code>, <code>two-marker</code>, <code>common</code>, <code>eas</code>, or <code>proxy</code></td>\n</tr>\n<tr>\n<td><code>--geno-mode</code></td>\n<td><code>auto</code></td>\n<td><code>auto</code>, <code>hardcall</code>, <code>dosage</code>, or <code>probability</code></td>\n</tr>\n<tr>\n<td><code>--phase</code></td>\n<td><code>auto</code></td>\n<td><code>auto</code>, <code>phased</code>, or <code>unphased</code></td>\n</tr>\n<tr>\n<td><code>--assume-trans</code> / <code>--no-assume-trans</code></td>\n<td>trans on</td>\n<td>Unphased double-het (rs601338 × rs1047781): assign <code>Se^w/se</code> (default) or leave ambiguous</td>\n</tr>\n<tr>\n<td><code>--phenotype-coding</code></td>\n<td><code>biochemical</code></td>\n<td><code>biochemical</code> (default) or <code>gwas</code></td>\n</tr>\n<tr>\n<td><code>--min-genotype-prob</code></td>\n<td><code>0.90</code></td>\n<td>Minimum max(GP) for a probability hardcall</td>\n</tr>\n<tr>\n<td><code>--dosage-hardcall-threshold</code></td>\n<td><code>0.1</code></td>\n<td>Dosage rounding window around 0 / 1 / 2</td>\n</tr>\n<tr>\n<td><code>--strict-method</code></td>\n<td>off</td>\n<td>Fail if the requested method's markers are missing</td>\n</tr>\n<tr>\n<td><code>--inspect</code></td>\n<td>off</td>\n<td>Probe markers and recommended method; do not write calls</td>\n</tr>\n<tr>\n<td><code>--version</code></td>\n<td>—</td>\n<td>Print the package version and exit</td>\n</tr>\n<tr>\n<td><code>--methods</code></td>\n<td>—</td>\n<td>List methods (no data file)</td>\n</tr>\n<tr>\n<td><code>--method-info NAME</code></td>\n<td>—</td>\n<td>Print citations for a method (no data file)</td>\n</tr>\n<tr>\n<td><code>--report</code></td>\n<td><code>PREFIX.report.html</code></td>\n<td>HTML run report path</td>\n</tr>\n</tbody>\n</table>\n<p><code>--method auto</code> picks the first method whose markers are present: <code>two-marker</code> → <code>common</code> → <code>eas</code> → <code>proxy</code>. <code>--phenotype-coding gwas</code> recodes <code>Se^w/Se^w</code> and <code>Se^w/se</code> as non-secretor; <code>fut2_genotype</code> still keeps <code>Se^w</code>. See <a href=\"../methods/\">Inference methods</a>.</p>\n<p><code>--geno-mode auto</code> uses GP, then DS, then hardcall GT. <code>--phase auto</code> uses phased haplotypes when the file has <code>|</code> genotypes; otherwise it enumerates unphased diplotypes. <code>--build auto</code> uses marker coordinates, header metadata, and chromosome lengths; conflicting evidence is an error and requires explicit <code>--build</code>.</p>\n<h2 id=\"inspect-and-method-metadata\">Inspect and method metadata<a class=\"headerlink\" href=\"#inspect-and-method-metadata\" title=\"Permanent link\">&para;</a></h2>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-3-1\"><a id=\"__codelineno-3-1\" name=\"__codelineno-3-1\" href=\"#__codelineno-3-1\"></a>genosecretor<span class=\"w\"> </span>--version\n</span><span id=\"__span-3-2\"><a id=\"__codelineno-3-2\" name=\"__codelineno-3-2\" href=\"#__codelineno-3-2\"></a>genosecretor<span class=\"w\"> </span>cohort.pgen<span class=\"w\"> </span>--inspect\n</span><span id=\"__span-3-3\"><a id=\"__codelineno-3-3\" name=\"__codelineno-3-3\" href=\"#__codelineno-3-3\"></a>genosecretor<span class=\"w\"> </span>--methods\n</span><span id=\"__span-3-4\"><a id=\"__codelineno-3-4\" name=\"__codelineno-3-4\" href=\"#__codelineno-3-4\"></a>genosecretor<span class=\"w\"> </span>--method-info<span class=\"w\"> </span>two-marker\n</span></code></pre></div>\n<p><code>--inspect</code> reports which FUT2 tags were found, call rates, genome build, and the recommended method. <code>--methods</code> and <code>--method-info</code> do not require an input file.</p>\n<h2 id=\"input-formats\">Input formats<a class=\"headerlink\" href=\"#input-formats\" title=\"Permanent link\">&para;</a></h2>\n<table>\n<thead>\n<tr>\n<th>Format</th>\n<th>Extensions</th>\n<th>Notes</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>VCF/BCF</td>\n<td><code>.vcf</code>, <code>.vcf.gz</code>, <code>.bcf</code></td>\n<td>GT, phased GT, DS, GP</td>\n</tr>\n<tr>\n<td>PLINK2</td>\n<td><code>.pgen</code> + <code>.pvar</code> + <code>.psam</code></td>\n<td>Auto-locates companion files</td>\n</tr>\n<tr>\n<td>PLINK1</td>\n<td><code>.bed</code> + <code>.bim</code> + <code>.fam</code></td>\n<td><code>--format plink1</code></td>\n</tr>\n<tr>\n<td>BGEN</td>\n<td><code>.bgen</code> + <code>.sample</code></td>\n<td>Dosage/probability support</td>\n</tr>\n</tbody>\n</table>\n<p>GRCh37/hg19, GRCh38/hg38, and T2T-CHM13v2 are supported.</p>\n<h2 id=\"outputs\">Outputs<a class=\"headerlink\" href=\"#outputs\" title=\"Permanent link\">&para;</a></h2>\n<p>A successful call writes four files:</p>\n<table>\n<thead>\n<tr>\n<th>File</th>\n<th>Contents</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td><code>PREFIX.secretor.tsv</code></td>\n<td>Per-sample secretor calls</td>\n</tr>\n<tr>\n<td><code>PREFIX.qc.tsv</code></td>\n<td>Run-level QC metrics</td>\n</tr>\n<tr>\n<td><code>PREFIX.summary.txt</code></td>\n<td>Human-readable summary</td>\n</tr>\n<tr>\n<td><code>PREFIX.report.html</code></td>\n<td>HTML run report (<code>--report</code> overrides the path)</td>\n</tr>\n</tbody>\n</table>\n<p><code>.secretor.tsv</code> columns:</p>\n<table>\n<thead>\n<tr>\n<th>Column</th>\n<th>Description</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>FID</td>\n<td>Family or cohort identifier from the input file</td>\n</tr>\n<tr>\n<td>IID</td>\n<td>Individual sample identifier</td>\n</tr>\n<tr>\n<td>secretor_status</td>\n<td>Inferred phenotype: secretor, weak-secretor, non-secretor, or unknown (GWAS coding recodes weak-secretor as non-secretor)</td>\n</tr>\n<tr>\n<td>fut2_genotype</td>\n<td>Diplotype label (for example Se/se), or ambiguous</td>\n</tr>\n<tr>\n<td>fut2_allele1</td>\n<td>First haplotype allele after sort (Se &lt; Se^w &lt; se)</td>\n</tr>\n<tr>\n<td>fut2_allele2</td>\n<td>Second haplotype allele after sort</td>\n</tr>\n<tr>\n<td>haplotype1</td>\n<td>Haplotype call on chromosome copy 1</td>\n</tr>\n<tr>\n<td>haplotype2</td>\n<td>Haplotype call on chromosome copy 2</td>\n</tr>\n<tr>\n<td>method</td>\n<td>Inference method used for this sample</td>\n</tr>\n<tr>\n<td>geno_mode</td>\n<td>Genotype interpretation mode (hardcall, dosage, probability, auto)</td>\n</tr>\n<tr>\n<td>phase_mode</td>\n<td>Whether haplotypes used phase (phased) or enumeration (unphased)</td>\n</tr>\n<tr>\n<td>build</td>\n<td>Genome assembly used for marker coordinates</td>\n</tr>\n<tr>\n<td>confidence</td>\n<td>high, medium, low, or none (not a calibrated probability)</td>\n</tr>\n<tr>\n<td>qc_status</td>\n<td>PASS, AMBIGUOUS, MISSING_MARKER, CONFLICT, or LOW_CONFIDENCE</td>\n</tr>\n<tr>\n<td>qc_reason</td>\n<td>Free-text explanation of QC status</td>\n</tr>\n<tr>\n<td>possible_diplotypes</td>\n<td>Compatible diplotypes when fut2_genotype is ambiguous</td>\n</tr>\n</tbody>\n</table>\n<p>See <a href=\"../workflow/\">Workflow</a> for how genotypes move from file load to these files.</p>\n<h2 id=\"python-api\">Python API<a class=\"headerlink\" href=\"#python-api\" title=\"Permanent link\">&para;</a></h2>\n<p><code>SecretorCaller</code> constructor kwargs match the CLI. <code>call()</code> returns a <code>CallerResult</code>; iterate <code>result.calls</code> for per-sample fields.</p>\n<div class=\"language-python highlight\"><pre><span></span><code><span id=\"__span-4-1\"><a id=\"__codelineno-4-1\" name=\"__codelineno-4-1\" href=\"#__codelineno-4-1\"></a><span class=\"kn\">from</span><span class=\"w\"> </span><span class=\"nn\">genosecretor</span><span class=\"w\"> </span><span class=\"kn\">import</span> <span class=\"n\">SecretorCaller</span>\n</span><span id=\"__span-4-2\"><a id=\"__codelineno-4-2\" name=\"__codelineno-4-2\" href=\"#__codelineno-4-2\"></a>\n</span><span id=\"__span-4-3\"><a id=\"__codelineno-4-3\" name=\"__codelineno-4-3\" href=\"#__codelineno-4-3\"></a><span class=\"n\">caller</span> <span class=\"o\">=</span> <span class=\"n\">SecretorCaller</span><span class=\"p\">(</span>\n</span><span id=\"__span-4-4\"><a id=\"__codelineno-4-4\" name=\"__codelineno-4-4\" href=\"#__codelineno-4-4\"></a>    <span class=\"n\">method</span><span class=\"o\">=</span><span class=\"s2\">&quot;auto&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-5\"><a id=\"__codelineno-4-5\" name=\"__codelineno-4-5\" href=\"#__codelineno-4-5\"></a>    <span class=\"n\">build</span><span class=\"o\">=</span><span class=\"s2\">&quot;auto&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-6\"><a id=\"__codelineno-4-6\" name=\"__codelineno-4-6\" href=\"#__codelineno-4-6\"></a>    <span class=\"n\">genotype_mode</span><span class=\"o\">=</span><span class=\"s2\">&quot;auto&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-7\"><a id=\"__codelineno-4-7\" name=\"__codelineno-4-7\" href=\"#__codelineno-4-7\"></a>    <span class=\"n\">phase</span><span class=\"o\">=</span><span class=\"s2\">&quot;auto&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-8\"><a id=\"__codelineno-4-8\" name=\"__codelineno-4-8\" href=\"#__codelineno-4-8\"></a>    <span class=\"nb\">format</span><span class=\"o\">=</span><span class=\"s2\">&quot;auto&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-9\"><a id=\"__codelineno-4-9\" name=\"__codelineno-4-9\" href=\"#__codelineno-4-9\"></a>    <span class=\"n\">dosage_threshold</span><span class=\"o\">=</span><span class=\"mf\">0.1</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-10\"><a id=\"__codelineno-4-10\" name=\"__codelineno-4-10\" href=\"#__codelineno-4-10\"></a>    <span class=\"n\">min_genotype_prob</span><span class=\"o\">=</span><span class=\"mf\">0.9</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-11\"><a id=\"__codelineno-4-11\" name=\"__codelineno-4-11\" href=\"#__codelineno-4-11\"></a>    <span class=\"n\">strict_method</span><span class=\"o\">=</span><span class=\"kc\">False</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-12\"><a id=\"__codelineno-4-12\" name=\"__codelineno-4-12\" href=\"#__codelineno-4-12\"></a>    <span class=\"n\">assume_trans</span><span class=\"o\">=</span><span class=\"kc\">True</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-13\"><a id=\"__codelineno-4-13\" name=\"__codelineno-4-13\" href=\"#__codelineno-4-13\"></a>    <span class=\"n\">phenotype_coding</span><span class=\"o\">=</span><span class=\"s2\">&quot;biochemical&quot;</span><span class=\"p\">,</span>\n</span><span id=\"__span-4-14\"><a id=\"__codelineno-4-14\" name=\"__codelineno-4-14\" href=\"#__codelineno-4-14\"></a><span class=\"p\">)</span>\n</span><span id=\"__span-4-15\"><a id=\"__codelineno-4-15\" name=\"__codelineno-4-15\" href=\"#__codelineno-4-15\"></a><span class=\"n\">result</span> <span class=\"o\">=</span> <span class=\"n\">caller</span><span class=\"o\">.</span><span class=\"n\">call</span><span class=\"p\">(</span><span class=\"s2\">&quot;ukb.pgen&quot;</span><span class=\"p\">)</span>\n</span><span id=\"__span-4-16\"><a id=\"__codelineno-4-16\" name=\"__codelineno-4-16\" href=\"#__codelineno-4-16\"></a><span class=\"k\">for</span> <span class=\"n\">call</span> <span class=\"ow\">in</span> <span class=\"n\">result</span><span class=\"o\">.</span><span class=\"n\">calls</span><span class=\"p\">:</span>\n</span><span id=\"__span-4-17\"><a id=\"__codelineno-4-17\" name=\"__codelineno-4-17\" href=\"#__codelineno-4-17\"></a>    <span class=\"nb\">print</span><span class=\"p\">(</span><span class=\"n\">call</span><span class=\"o\">.</span><span class=\"n\">sample</span><span class=\"o\">.</span><span class=\"n\">iid</span><span class=\"p\">,</span> <span class=\"n\">call</span><span class=\"o\">.</span><span class=\"n\">secretor_status</span><span class=\"p\">,</span> <span class=\"n\">call</span><span class=\"o\">.</span><span class=\"n\">fut2_genotype</span><span class=\"p\">)</span>\n</span></code></pre></div>\n<p>Inspect without writing calls:</p>\n<div class=\"language-python highlight\"><pre><span></span><code><span id=\"__span-5-1\"><a id=\"__codelineno-5-1\" name=\"__codelineno-5-1\" href=\"#__codelineno-5-1\"></a><span class=\"n\">result</span> <span class=\"o\">=</span> <span class=\"n\">caller</span><span class=\"o\">.</span><span class=\"n\">call</span><span class=\"p\">(</span><span class=\"s2\">&quot;ukb.pgen&quot;</span><span class=\"p\">,</span> <span class=\"n\">inspect_only</span><span class=\"o\">=</span><span class=\"kc\">True</span><span class=\"p\">)</span>\n</span><span id=\"__span-5-2\"><a id=\"__codelineno-5-2\" name=\"__codelineno-5-2\" href=\"#__codelineno-5-2\"></a><span class=\"nb\">print</span><span class=\"p\">(</span><span class=\"n\">result</span><span class=\"o\">.</span><span class=\"n\">build</span><span class=\"p\">,</span> <span class=\"n\">result</span><span class=\"o\">.</span><span class=\"n\">method</span><span class=\"p\">,</span> <span class=\"n\">result</span><span class=\"o\">.</span><span class=\"n\">inspect</span><span class=\"p\">)</span>\n</span></code></pre></div>\n<h2 id=\"see-also\">See also<a class=\"headerlink\" href=\"#see-also\" title=\"Permanent link\">&para;</a></h2>\n<ul>\n<li><a href=\"../workflow/\">Workflow</a> — load-to-output pipeline</li>\n<li><a href=\"../methods/\">Inference methods</a> — haplotype and phenotype rules</li>\n<li><a href=\"../markers/\">Markers</a> — coordinates and 1000 Genomes LD r²</li>\n<li><a href=\"../assumptions/\">Assumptions</a> — limitations</li>\n<li><a href=\"../examples/\">Examples</a> — synthetic and 1000 Genomes demos</li>\n</ul>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n                \n              </article>\n            </div>\n          \n          \n  <script>var tabs=__md_get(\"__tabs\");if(Array.isArray(tabs))e:for(var set of document.querySelectorAll(\".tabbed-set\")){var 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genosecretor-0.1.0/.cache/13584948190430787628

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       </div>\n            \n          \n          \n            <div class=\"md-content\" data-md-component=\"content\">\n              \n              <article class=\"md-content__inner md-typeset\">\n                \n                  \n  \n  \n\n\n<h1 id=\"1000-genomes-assume-trans-check\">1000 Genomes <code>--assume-trans</code> check<a class=\"headerlink\" href=\"#1000-genomes-assume-trans-check\" title=\"Permanent link\">&para;</a></h1>\n<p>Phased NYGC 30x GRCh38 panels (AFR, AMR, EAS, EUR) as cis/trans truth for the unphased double-heterozygote rule.</p>\n<div class=\"admonition warning\">\n<p class=\"admonition-title\">Research use only</p>\n<p>Phased 1000 Genomes genotypes are not salivary secretor phenotypes. This check asks whether\nunphased <code>--assume-trans</code> matches <strong>phase</strong> at rs601338 × rs1047781. It is not a clinical\nvalidation.</p>\n</div>\n<p>Panels: <code>~/.gwaslab/{ANC}.ALL.split_norm_af.1kg_30x.hg38.vcf.gz</code> (override with <code>GENOSECRETOR_1KG_&lt;ANC&gt;_VCF</code>). AFR/EAS/EUR fall back to the bundled extracts if the full panel is absent.</p>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-0-1\"><a id=\"__codelineno-0-1\" name=\"__codelineno-0-1\" href=\"#__codelineno-0-1\"></a><span class=\"ch\">#!/usr/bin/env bash</span>\n</span><span id=\"__span-0-2\"><a id=\"__codelineno-0-2\" name=\"__codelineno-0-2\" href=\"#__codelineno-0-2\"></a><span class=\"c1\"># Compare unphased --assume-trans to phased 1KG AFR/AMR/EAS/EUR diplotypes.</span>\n</span><span id=\"__span-0-3\"><a id=\"__codelineno-0-3\" name=\"__codelineno-0-3\" href=\"#__codelineno-0-3\"></a><span class=\"c1\"># Panels: GENOSECRETOR_1KG_&lt;ANC&gt;_VCF, else ~/.gwaslab/&lt;ANC&gt;.ALL.split_norm_af.1kg_30x.hg38.vcf.gz</span>\n</span><span id=\"__span-0-4\"><a id=\"__codelineno-0-4\" name=\"__codelineno-0-4\" href=\"#__codelineno-0-4\"></a><span class=\"c1\"># AFR/EAS/EUR fall back to the bundled three-SNP extracts.</span>\n</span><span id=\"__span-0-5\"><a id=\"__codelineno-0-5\" name=\"__codelineno-0-5\" href=\"#__codelineno-0-5\"></a><span class=\"nb\">set</span><span class=\"w\"> </span>-euo<span class=\"w\"> </span>pipefail\n</span><span id=\"__span-0-6\"><a id=\"__codelineno-0-6\" name=\"__codelineno-0-6\" href=\"#__codelineno-0-6\"></a><span class=\"nv\">ROOT</span><span class=\"o\">=</span><span class=\"s2\">&quot;</span><span class=\"k\">$(</span><span class=\"nb\">cd</span><span class=\"w\"> </span><span class=\"s2\">&quot;</span><span class=\"k\">$(</span>dirname<span class=\"w\"> </span><span class=\"s2\">&quot;</span><span class=\"nv\">$0</span><span class=\"s2\">&quot;</span><span class=\"k\">)</span><span class=\"s2\">&quot;</span><span class=\"w\"> </span><span class=\"o\">&amp;&amp;</span><span class=\"w\"> </span><span class=\"nb\">pwd</span><span class=\"k\">)</span><span class=\"s2\">&quot;</span>\n</span><span id=\"__span-0-7\"><a id=\"__codelineno-0-7\" name=\"__codelineno-0-7\" href=\"#__codelineno-0-7\"></a>mkdir<span class=\"w\"> </span>-p<span class=\"w\"> </span><span class=\"s2\">&quot;</span><span class=\"nv\">$ROOT</span><span class=\"s2\">/out&quot;</span>\n</span><span id=\"__span-0-8\"><a id=\"__codelineno-0-8\" name=\"__codelineno-0-8\" href=\"#__codelineno-0-8\"></a>python<span class=\"w\"> </span><span class=\"s2\">&quot;</span><span class=\"nv\">$ROOT</span><span class=\"s2\">/verify_assume_trans_1kg.py&quot;</span><span class=\"w\"> </span>--out-dir<span class=\"w\"> </span><span class=\"s2\">&quot;</span><span class=\"nv\">$ROOT</span><span class=\"s2\">/out&quot;</span>\n</span><span id=\"__span-0-9\"><a id=\"__codelineno-0-9\" name=\"__codelineno-0-9\" href=\"#__codelineno-0-9\"></a><span class=\"nb\">echo</span><span class=\"w\"> </span><span class=\"s2\">&quot;Summary: </span><span class=\"nv\">$ROOT</span><span class=\"s2\">/out/assume_trans_1kg.summary.txt&quot;</span>\n</span></code></pre></div>\n<div class=\"language-bash highlight\"><pre><span></span><code><span id=\"__span-1-1\"><a id=\"__codelineno-1-1\" name=\"__codelineno-1-1\" href=\"#__codelineno-1-1\"></a>./examples/run_1kg_assume_trans.sh\n</span></code></pre></div>\n<p>Writes <code>examples/out/assume_trans_1kg.summary.tsv</code>, <code>.discordant.tsv</code>, and <code>.summary.txt</code>.</p>\n<h2 id=\"operational-metric-the-flag\">Operational metric (the flag)<a class=\"headerlink\" href=\"#operational-metric-the-flag\" title=\"Permanent link\">&para;</a></h2>\n<p>Unphased heterozygotes at <strong>both</strong> functional SNPs are compatible with trans <code>Se^w/se</code> or cis <code>Se/se</code> (both variants on one haplotype). <code>--no-assume-trans</code> leaves those samples ambiguous; default <code>--assume-trans</code> assigns <strong><code>Se^w/se</code></strong>. Concordance is the fraction of that double-het set whose <strong>phased</strong> genotype is <code>Se^w/se</code>.</p>\n<table>\n<thead>\n<tr>\n<th>Super-population</th>\n<th>n</th>\n<th>Double-het</th>\n<th>Phased trans (<code>Se^w/se</code>)</th>\n<th>Phased cis (<code>Se/se</code>)</th>\n<th>Concordance</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>AFR</td>\n<td>661</td>\n<td>0</td>\n<td>0</td>\n<td>0</td>\n<td>NA</td>\n</tr>\n<tr>\n<td>AMR</td>\n<td>347</td>\n<td>0</td>\n<td>0</td>\n<td>0</td>\n<td>NA</td>\n</tr>\n<tr>\n<td>EAS</td>\n<td>504</td>\n<td>1</td>\n<td>1</td>\n<td>0</td>\n<td>1/1 (100%)</td>\n</tr>\n<tr>\n<td>EUR</td>\n<td>503</td>\n<td>0</td>\n<td>0</td>\n<td>0</td>\n<td>NA</td>\n</tr>\n</tbody>\n</table>\n<p>se428 and se385 are nearly mutually exclusive in these panels, so the unphased rule almost never fires. The one EAS double-het is trans in phase, so <code>--assume-trans</code> matches the phased diplotype (and phenotype). Zero mismatches vs phase in AFR/AMR/EAS/EUR.</p>\n<p>Default <code>--assume-trans</code> is unchanged. Pass <code>--no-assume-trans</code> when you do not want the ancestral-haplotype assumption.</p>\n<h2 id=\"haplotype-metric\">Haplotype metric<a class=\"headerlink\" href=\"#haplotype-metric\" title=\"Permanent link\">&para;</a></h2>\n<p>Phased haplotype counts (<code>se</code> = se428 LoF, <code>Se^w</code> = se385 weak, <code>Se</code> = functional):</p>\n<table>\n<thead>\n<tr>\n<th>Super-population</th>\n<th>se</th>\n<th>Se^w</th>\n<th>Se</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>AFR</td>\n<td>649</td>\n<td>0</td>\n<td>673</td>\n</tr>\n<tr>\n<td>AMR</td>\n<td>237</td>\n<td>1</td>\n<td>456</td>\n</tr>\n<tr>\n<td>EAS</td>\n<td>4</td>\n<td>443</td>\n<td>561</td>\n</tr>\n<tr>\n<td>EUR</td>\n<td>444</td>\n<td>0</td>\n<td>562</td>\n</tr>\n</tbody>\n</table>\n<p>se385 (<code>Se^w</code>) is common only in EAS. AFR and EUR have no <code>Se^w</code> haplotypes here; AMR has a single copy. That is why double-hets are rare: the two derived alleles almost never co-occur in the same person.</p>\n<p>See <a href=\"../../assumptions/\">Assumptions</a> and <a href=\"../../methods/\">Inference methods</a> (double-heterozygote resolution).</p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n                \n              </article>\n            </div>\n          \n          \n  <script>var tabs=__md_get(\"__tabs\");if(Array.isArray(tabs))e:for(var set of document.querySelectorAll(\".tabbed-set\")){var labels=set.querySelector(\".tabbed-labels\");for(var tab of tabs)for(var label of labels.getElementsByTagName(\"label\"))if(label.innerText.trim()===tab){var input=document.getElementById(label.htmlFor);input.checked=!0;continue e}}</script>\n\n<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith(\"__tabbed_\"))</script>\n        </div>\n        \n          <button type=\"button\" class=\"md-top md-icon\" data-md-component=\"top\" hidden>\n  \n  <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-circle-arrow-up\" viewBox=\"0 0 24 24\"><circle cx=\"12\" cy=\"12\" r=\"10\"/><path d=\"m16 12-4-4-4 4M12 16V8\"/></svg>\n  Back to top\n</button>\n        \n      </main>\n      \n        <footer class=\"md-footer\">\n  \n    \n      \n      <nav class=\"md-footer__inner md-grid\" aria-label=\"Footer\" >\n        \n          \n          <a href=\"../1kg/\" class=\"md-footer__link md-footer__link--prev\" aria-label=\"Previous: 1000 Genomes\">\n            <div class=\"md-footer__button md-icon\">\n              \n              <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-arrow-left\" viewBox=\"0 0 24 24\"><path d=\"m12 19-7-7 7-7M19 12H5\"/></svg>\n            </div>\n            <div class=\"md-footer__title\">\n              <span class=\"md-footer__direction\">\n                Previous\n              </span>\n              <div class=\"md-ellipsis\">\n                1000 Genomes\n              </div>\n            </div>\n          </a>\n        \n        \n          \n          <a href=\"../report/\" class=\"md-footer__link md-footer__link--next\" aria-label=\"Next: Example reports\">\n            <div class=\"md-footer__title\">\n              <span class=\"md-footer__direction\">\n                Next\n              </span>\n              <div class=\"md-ellipsis\">\n                Example reports\n              </div>\n            </div>\n            <div class=\"md-footer__button md-icon\">\n              \n              <svg xmlns=\"http://www.w3.org/2000/svg\" fill=\"none\" stroke=\"currentColor\" stroke-linecap=\"round\" stroke-linejoin=\"round\" stroke-width=\"2\" class=\"lucide lucide-arrow-right\" viewBox=\"0 0 24 24\"><path d=\"M5 12h14M12 5l7 7-7 7\"/></svg>\n            </div>\n          </a>\n        \n      </nav>\n    \n  \n  <div class=\"md-footer-meta md-typeset\">\n    <div class=\"md-footer-meta__inner md-grid\">\n      <div class=\"md-copyright\">\n  \n    <div class=\"md-copyright__highlight\">\n      Copyright &copy; 2026 Yunye He\n    </div>\n  \n  \n    Made with\n    <a href=\"https://zensical.org/\" target=\"_blank\" rel=\"noopener\">\n      Zensical\n    </a>\n  \n</div>\n      \n        \n<div class=\"md-social\">\n  \n    \n    \n    \n    \n      \n      \n    \n    <a href=\"https://github.com/cloufield/genoSecretor\" target=\"_blank\" rel=\"noopener\" title=\"github.com\" class=\"md-social__link\">\n      <svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 512 512\"><!--! 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