-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathSNV.html
More file actions
189 lines (166 loc) · 10 KB
/
Copy pathSNV.html
File metadata and controls
189 lines (166 loc) · 10 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>SNV Analysis — baseq 0.01 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="DropSeq" href="Drops.html" />
<link rel="prev" title="CNV Analysis" href="CNV.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="snv-analysis">
<span id="snv"></span><h1>SNV Analysis<a class="headerlink" href="#snv-analysis" title="Permalink to this headline">¶</a></h1>
<p>SNV analysis functions.</p>
<div class="section" id="quality-control">
<h2>Quality Control<a class="headerlink" href="#quality-control" title="Permalink to this headline">¶</a></h2>
<div class="section" id="module-baseq.snv.qc.enrich">
<span id="enrichment"></span><h3>Enrichment<a class="headerlink" href="#module-baseq.snv.qc.enrich" title="Permalink to this headline">¶</a></h3>
<dl class="function">
<dt id="baseq.snv.qc.enrich.enrich_qc">
<code class="descclassname">baseq.snv.qc.enrich.</code><code class="descname">enrich_qc</code><span class="sig-paren">(</span><em>samplename</em>, <em>bampath</em>, <em>intervals</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/qc/enrich.html#enrich_qc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.qc.enrich.enrich_qc" title="Permalink to this definition">¶</a></dt>
<dd><p>Check the coverage depth and enrichment quality.</p>
<p>Usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">enrich_qc</span><span class="p">(</span><span class="s2">"sample01"</span><span class="p">,</span> <span class="s2">"xx.bam"</span><span class="p">,</span> <span class="s2">"panel.bed"</span><span class="p">)</span>
</pre></div>
</div>
<dl class="docutils">
<dt>Return:</dt>
<dd>Sample/Total/Mapped/Map_Ratio/Dup_ratio/PCT_10X/PCT_30X/…</dd>
</dl>
</dd></dl>
</div>
</div>
<div class="section" id="vcf">
<h2>VCF<a class="headerlink" href="#vcf" title="Permalink to this headline">¶</a></h2>
<div class="section" id="module-baseq.snv.vcf.GATK">
<span id="vcf-stats-and-filter"></span><h3>VCF stats and Filter<a class="headerlink" href="#module-baseq.snv.vcf.GATK" title="Permalink to this headline">¶</a></h3>
<dl class="function">
<dt id="baseq.snv.vcf.GATK.vcf_stats">
<code class="descclassname">baseq.snv.vcf.GATK.</code><code class="descname">vcf_stats</code><span class="sig-paren">(</span><em>sample</em>, <em>vcfpath</em>, <em>min_depth=50</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/vcf/GATK.html#vcf_stats"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.vcf.GATK.vcf_stats" title="Permalink to this definition">¶</a></dt>
<dd><p>Stats on the VCF from GATK</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">vcf_stats</span><span class="p">(</span><span class="s2">"sample1"</span><span class="p">,</span> <span class="s2">"path/to/vcf"</span><span class="p">,</span> <span class="n">min_depth</span><span class="o">=</span><span class="mi">30</span><span class="p">)</span>
</pre></div>
</div>
<dl class="docutils">
<dt>Return:</dt>
<dd>A dict/json containing:
Samplename/counts/mean_depth/GT_01/GT_11/MAF
MAF is minor allel frequency.</dd>
</dl>
</dd></dl>
</div>
</div>
<div class="section" id="gatk">
<h2>GATK<a class="headerlink" href="#gatk" title="Permalink to this headline">¶</a></h2>
<div class="section" id="module-baseq.snv.gatk">
<span id="run-gatk"></span><h3>run GATK<a class="headerlink" href="#module-baseq.snv.gatk" title="Permalink to this headline">¶</a></h3>
<dl class="function">
<dt id="baseq.snv.gatk.alignment">
<code class="descclassname">baseq.snv.gatk.</code><code class="descname">alignment</code><span class="sig-paren">(</span><em>fq1</em>, <em>fq2</em>, <em>sample</em>, <em>genome</em>, <em>outfile</em>, <em>thread=8</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/gatk.html#alignment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.gatk.alignment" title="Permalink to this definition">¶</a></dt>
<dd><p>Map fastq1/2 files into genome using BWA. Add tags to bamfile using the input sample name. The bamfile is named as outfile.</p>
</dd></dl>
<dl class="function">
<dt id="baseq.snv.gatk.bqsr">
<code class="descclassname">baseq.snv.gatk.</code><code class="descname">bqsr</code><span class="sig-paren">(</span><em>markedbam</em>, <em>bqsrbam</em>, <em>genome</em>, <em>disable_dup_filter=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/gatk.html#bqsr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.gatk.bqsr" title="Permalink to this definition">¶</a></dt>
<dd><p>Run <a class="reference external" href="https://gatkforums.broadinstitute.org/gatk/discussion/44/base-quality-score-recalibration-bqsr">BQSR</a>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">bqsr</span><span class="p">()</span>
<span class="n">This</span> <span class="n">will</span> <span class="n">generate</span> <span class="n">a</span> <span class="n">XXXX</span><span class="o">...</span>
</pre></div>
</div>
</dd></dl>
<dl class="function">
<dt id="baseq.snv.gatk.run_markdup">
<code class="descclassname">baseq.snv.gatk.</code><code class="descname">run_markdup</code><span class="sig-paren">(</span><em>bamfile</em>, <em>markedbam</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/gatk.html#run_markdup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.gatk.run_markdup" title="Permalink to this definition">¶</a></dt>
<dd><p>Run MarkDuplicate of Picard. Generate the bai for the marked bamfile.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">run_markdup</span><span class="p">(</span><span class="s2">"in.bam"</span><span class="p">,</span> <span class="s2">"in.marked.bam"</span><span class="p">)</span>
</pre></div>
</div>
</dd></dl>
<dl class="function">
<dt id="baseq.snv.gatk.selectvar">
<code class="descclassname">baseq.snv.gatk.</code><code class="descname">selectvar</code><span class="sig-paren">(</span><em>rawvcf</em>, <em>selectvcf</em>, <em>filtervcf</em>, <em>genome</em>, <em>run=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/baseq/snv/gatk.html#selectvar"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#baseq.snv.gatk.selectvar" title="Permalink to this definition">¶</a></dt>
<dd><p>Select Variants, it process the XX from XX, genrate XX for XX…</p>
</dd></dl>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">SNV Analysis</a><ul>
<li><a class="reference internal" href="#quality-control">Quality Control</a><ul>
<li><a class="reference internal" href="#module-baseq.snv.qc.enrich">Enrichment</a></li>
</ul>
</li>
<li><a class="reference internal" href="#vcf">VCF</a><ul>
<li><a class="reference internal" href="#module-baseq.snv.vcf.GATK">VCF stats and Filter</a></li>
</ul>
</li>
<li><a class="reference internal" href="#gatk">GATK</a><ul>
<li><a class="reference internal" href="#module-baseq.snv.gatk">run GATK</a></li>
</ul>
</li>
</ul>
</li>
</ul>
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li>Previous: <a href="CNV.html" title="previous chapter">CNV Analysis</a></li>
<li>Next: <a href="Drops.html" title="next chapter">DropSeq</a></li>
</ul></li>
</ul>
</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/SNV.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
©2018, Xiannian Zhang.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.4</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
|
<a href="_sources/SNV.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>