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03_Data_formats/index.html

@@ -2735,7 +2735,7 @@ <h3 id="ped-map">ped / map</h3>
 <div class="admonition example">
 <p class="admonition-title"><code>.ped</code></p>
 <div class="highlight"><pre><span></span><code># check the first 16 rows and 16 columns of the ped file
-cut -d &quot; &quot; -f 1-16 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.ped | head
+cut -d &quot; &quot; -f 1-16 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.ped | head
 0 HG00403 0 0 0 -9 G G T T A A G A C C
 0 HG00404 0 0 0 -9 G G T T A A G A T C
 0 HG00406 0 0 0 -9 G G T T A A G A T C
@@ -2764,7 +2764,7 @@ <h3 id="ped-map">ped / map</h3>
 </ul>
 <div class="admonition example">
 <p class="admonition-title"><code>.map</code></p>
-<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.map
+<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.map
 1       1:13273:G:C     0       13273
 1       1:14599:T:A     0       14599
 1       1:14604:A:G     0       14604
@@ -2781,15 +2781,15 @@ <h3 id="ped-map">ped / map</h3>
 <h3 id="bed-fam-bim">bed / fam /bim</h3>
 <p>bed/fam/bim formats are the binary implementation of ped/map formats.
 bed/bim/fam files contain the same information as ped/map but are much smaller in size.</p>
-<div class="highlight"><pre><span></span><code>-rw-r----- 1 yunye yunye 135M Dec 23 11:45 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.bed
--rw-r----- 1 yunye yunye  36M Dec 23 11:46 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.bim
--rw-r----- 1 yunye yunye 9.4K Dec 23 11:46 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.fam
--rw-r--r-- 1 yunye yunye  32M Dec 27 17:51 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.map
--rw-r--r-- 1 yunye yunye 2.2G Dec 27 17:51 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.ped
+<div class="highlight"><pre><span></span><code>-rw-r----- 1 yunye yunye 135M Dec 23 11:45 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.bed
+-rw-r----- 1 yunye yunye  36M Dec 23 11:46 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.bim
+-rw-r----- 1 yunye yunye 9.4K Dec 23 11:46 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.fam
+-rw-r--r-- 1 yunye yunye  32M Dec 27 17:51 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.map
+-rw-r--r-- 1 yunye yunye 2.2G Dec 27 17:51 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.ped
 </code></pre></div>
 <div class="admonition example">
 <p class="admonition-title"><code>.fam</code></p>
-<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.fam
+<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.fam
 0 HG00403 0 0 0 -9
 0 HG00404 0 0 0 -9
 0 HG00406 0 0 0 -9
@@ -2804,7 +2804,7 @@ <h3 id="bed-fam-bim">bed / fam /bim</h3>
 </div>
 <div class="admonition example">
 <p class="admonition-title"><code>.bim</code></p>
-<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.bim
+<div class="highlight"><pre><span></span><code>head 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.bim
 1       1:13273:G:C     0       13273   C       G
 1       1:14599:T:A     0       14599   A       T
 1       1:14604:A:G     0       14604   G       A
@@ -2822,7 +2822,7 @@ <h3 id="bed-fam-bim">bed / fam /bim</h3>
 <p>"Primary representation of genotype calls at biallelic variants
 The first three bytes should be 0x6c, 0x1b, and 0x01 in that order.
 The rest of the file is a sequence of V blocks of N/4 (rounded up) bytes each, where V is the number of variants and N is the number of samples. The first block corresponds to the first marker in the .bim file, etc."
-<div class="highlight"><pre><span></span><code>hexdump -C 1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020.bed | head
+<div class="highlight"><pre><span></span><code>hexdump -C 1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing.bed | head
 00000000  6c 1b 01 ff ff bf bf ff  ff ff ef fb ff ff ff fe  |l...............|
 00000010  ff ff ff ff fb ff bb ff  ff fb af ff ff fe fb ff  |................|
 00000020  ff ff ff fe ff ff ff ff  ff bf ff ff ef ff ff ef  |................|

04_Data_QC/index.html

@@ -3017,47 +3017,68 @@ <h3 id="hardy-weinberg-equilibrium-exact-test">Hardy-Weinberg equilibrium exact
 <div class="admonition example">
 <p class="admonition-title">Calculate the Hardy-Weinberg equilibrium exact test statistics for a single SNP using Python</p>
 <p>This code is converted from <a href="https://github.com/jeremymcrae/snphwe/blob/master/src/snp_hwe.cpp">here</a> (Jeremy McRae) to python. Orginal citation: Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. AJHG 76: 887-893
-<div class="highlight"><pre><span></span><code>def snphwe(obs_hets, obs_hom1, obs_hom2):
-    obs_homr = min(obs_hom1, obs_hom2)
-    obs_homc = max(obs_hom1, obs_hom2)
-
-    rare = 2 * obs_homr + obs_hets
-    genotypes = obs_hets + obs_homc + obs_homr
-
-    probs = [0.0 for i in range(rare +1)]
-
-    mid = rare * (2 * genotypes - rare) // (2 * genotypes)
-    if mid % 2 != rare%2:
-        mid += 1
-
-    probs[mid] = 1.0
-    sum_p = 1 #probs[mid]
-
-    curr_homr = (rare - mid) // 2
-    curr_homc = genotypes - mid - curr_homr
-
-    for curr_hets in range(mid, 1, -2):
-        probs[curr_hets - 2] = probs[curr_hets] * curr_hets * (curr_hets - 1.0)/ (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0))
-        sum_p+= probs[curr_hets - 2]
-        curr_homr += 1
-        curr_homc += 1
-
-    curr_homr = (rare - mid) // 2
-    curr_homc = genotypes - mid - curr_homr
-
-    for curr_hets in range(mid, rare-1, 2):
-        probs[curr_hets + 2] = probs[curr_hets] * 4.0 * curr_homr * curr_homc/ ((curr_hets + 2.0) * (curr_hets + 1.0))
-        sum_p += probs[curr_hets + 2]
-        curr_homr -= 1
-        curr_homc -= 1
-
-    target = probs[obs_hets]
-    p_hwe = 0.0
-    for p in probs:
-        if p &lt;= target :
-            p_hwe += p / sum_p  
-
-    return min(p_hwe,1)
+<div class="highlight"><pre><span></span><code>def snphwe(obs_hets: int, obs_hom1: int, obs_hom2: int) -&gt; float:
+&quot;&quot;&quot;Calculate Hardy-Weinberg equilibrium exact test for a variant
+
+Args:
+    obs_hets (int): observed heterozygous number
+    obs_hom1 (int): first observed homozygous number
+    obs_hom2 (int): second observed homozygous number
+
+Returns:
+    float: Hardy-Weinberg equilibrium exact test p-value.
+
+    - P &gt; 0.05: No significant deviation from Hardy-Weinberg equilibrium (HWE).
+    - P ≤ 0.05: Significant deviation from HWE, which could be due to factors such as population stratification, inbreeding, genotyping errors, or natural selection.
+&quot;&quot;&quot;
+obs_minor_homs = min(obs_hom1, obs_hom2)
+obs_mijor_homs = max(obs_hom1, obs_hom2)
+
+rare = 2 * obs_minor_homs + obs_hets
+genotypes = obs_hets + obs_mijor_homs + obs_minor_homs
+
+probs = [0.0 for i in range(rare +1)]
+
+mid = rare * (2 * genotypes - rare) // (2 * genotypes)
+if mid % 2 != rare%2:
+    mid += 1
+
+probs[mid] = 1.0
+sum_p = 1 #probs[mid]
+
+curr_homr = (rare - mid) // 2
+curr_homc = genotypes - mid - curr_homr
+
+for curr_hets in range(mid, 1, -2):
+    probs[curr_hets - 2] = probs[curr_hets] * curr_hets * (curr_hets - 1.0)/ (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0))
+    sum_p+= probs[curr_hets - 2]
+    curr_homr += 1
+    curr_homc += 1
+
+curr_homr = (rare - mid) // 2
+curr_homc = genotypes - mid - curr_homr
+
+for curr_hets in range(mid, rare-1, 2):
+    probs[curr_hets + 2] = probs[curr_hets] * 4.0 * curr_homr * curr_homc/ ((curr_hets + 2.0) * (curr_hets + 1.0))
+    sum_p += probs[curr_hets + 2]
+    curr_homr -= 1
+    curr_homc -= 1
+
+target = probs[obs_hets]
+p_hwe = 0.0
+for p in probs:
+    if p &lt;= target :
+        p_hwe += p / sum_p  
+
+return min(p_hwe,1)
+
+if __name__ == &#39;__main__&#39;:
+# For an example, we had 502 samples. 
+# At position 1:14930:A:G, we count:
+#     + 407 heterozygous genotypes (signed 0|1 or 1|0).
+#     + 4 homozygous genotypes AA (signed 0|0)
+#     + 91 homozygous genotypes GG (signed 1|1)
+print(snphwe(407,4,91))
 </code></pre></div></p>
 </div>
 <div class="admonition example">

05_PCA/index.html

@@ -2508,8 +2508,8 @@ <h2 id="sample-codes">Sample codes</h2>
         --bfile ${plinkFile} \
         --threads ${threadnum} \
         --read-freq ${outPrefix}.acount \
-        --score ${outPrefix}.eigenvec.allele 2 5 header-read no-mean-imputation variance-standardize \
-        --score-col-nums 6-15 \
+        --score ${outPrefix}.eigenvec.allele 2 6 header-read no-mean-imputation variance-standardize \
+        --score-col-nums 7-16 \
         --out ${outPrefix}_projected
 </code></pre></div>
 </div>

07_Annotation/index.html

@@ -2335,7 +2335,7 @@ <h3 id="format-input-file">Format input file</h3>
 <p>We will only use the first 100000 variants as an example.</p>
 <div class="admonition example">
 <p class="admonition-title">annovar_input</p>
-<div class="highlight"><pre><span></span><code>awk<span class="w"> </span><span class="s1">&#39;NR&gt;1 &amp;&amp; NR&lt;100000 {print $1,$2,$2,$4,$5}&#39;</span><span class="w"> </span>../06_Association_tests/1kgeas.B1.glm.logistic.<span class="w">    </span>hybrid<span class="w"> </span>&gt;<span class="w"> </span>annovar_input.txt
+<div class="highlight"><pre><span></span><code>awk<span class="w"> </span><span class="s1">&#39;NR&gt;1 &amp;&amp; NR&lt;100000 {print $1,$2,$2,$4,$5}&#39;</span><span class="w"> </span>../06_Association_tests/1kgeas.B1.glm.firth<span class="w"> </span>&gt;<span class="w"> </span>annovar_input.txt
 </code></pre></div>
 <div class="highlight"><pre><span></span><code>head annovar_input.txt 
 1 13273 13273 G C

12_fine_mapping/index.html

@@ -2367,7 +2367,7 @@ <h2 id="ld-matrix-calculation">LD Matrix Calculation</h2>
 <p class="admonition-title">Example</p>
 <p><div class="highlight"><pre><span></span><code>#!/bin/bash
 
-plinkFile=&quot;../01_Dataset/1KG.EAS.auto.snp.norm.nodup.split.maf005.thinp020&quot;
+plinkFile=&quot;../01_Dataset/1KG.EAS.auto.snp.norm.nodup.split.rare002.common015.missing&quot;
 
 # LD r matrix
 plink \