updated docs

Author: sigven

README.md

@@ -55,7 +55,7 @@ A local installation of Python (it has been tested with [version 2.7.13](https:/
 
 1. Download and unpack the [latest release](https://github.com/sigven/pcgr/releases/latest)
 2. Download and unpack the data bundle (approx. 17Gb) in the PCGR directory
-   * Download [the latest data bundle](https://drive.google.com/file/d/0B8aYD2TJ472mRjkxMXVaNm1zQ1U/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number)
+   * Download [the latest data bundle](https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number)
    * Unpack the data bundle, e.g. through the following Unix command: `gzip -dc pcgr.databundle.GRCh37.YYYYMMDD.tgz | tar xvf -`
 
     A _data/_ folder within the _pcgr-X.X_ software folder should now have been produced

docs/_build/doctrees/annotation_resources.doctree

@@ -71,3 +71,40 @@ Cancer gene knowledge bases
    suppressor/oncogene database (November 2015)
 -  `Cancer Gene Cencus <http://cancer.sanger.ac.uk/cosmic/>`__ -
    (February 2017)
+
+Notes on variant annotation datasets
+------------------------------------
+
+Genome mapping
+~~~~~~~~~~~~~~
+
+A requirement for all variant annotation datasets used in PCGR is that
+they have been mapped unambiguously to the human genome (GRCh37). For
+most datasets this is already the case (i.e. dbSNP, COSMIC, ClinVar
+etc.). A significant proportion of variants in the annotation datasets
+related to clinical interpretation, CIViC and CBMDB, are however not
+mapped to the genome. Whenever possible, we have utilized
+`TransVar <http://bioinformatics.mdanderson.org/transvarweb/>`__ to
+identify the actual genomic variants (e.g. *g.chr7:140453136A>T*) that
+corresponds to variants reported with other HGVS nomenclature (e.g.
+*p.V600E*).
+
+Other data quality concerns
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+**Clinical biomarkers** Clinical biomarkers included in PCGR is limited
+to the following: \* Markers reported at the variant level (e.g. **BRAF
+p.V600E**) \* Markers reported at the codon level (e.g. **KRAS p.G12**)
+\* Markers reported at the exon level (e.g. **KIT exon 11 mutation**) \*
+Within CBMDB, only markers collected from FDA/NCCN guidelines,
+scientific literature and clinical trials are included (markers
+collected from conference abstracts are not included)
+
+**COSMIC variants** The COSMIC dataset that is part of the PCGR
+annotation bundle is the subset of variants that satisfy the following
+criteria: \* **Mutation somatic status** is either
+'*confirmed\_somatic*' or
+'*reported\_in\_another\_cancer\_sample\_as\_somatic*'. \*
+**Site/histology** must be known and the sample must come from a
+malignant tumor (i.e. not polyps/adenomas, which are also found in
+COSMIC)

docs/_build/doctrees/environment.pickle

@@ -49,7 +49,7 @@ Download PCGR
    directory
 
    -  Download `the latest data
-      bundle <https://drive.google.com/file/d/0B8aYD2TJ472mRjkxMXVaNm1zQ1U/>`__
+      bundle <https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/>`__
       from Google Drive to ``~/pcgr-X.X`` (replace *X.X* with the
       version number)
    -  Decompress and untar the bundle, e.g. through the following Unix

docs/_build/doctrees/getting_started.doctree

@@ -96,6 +96,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting started</a></li>
 <li class="toctree-l1"><a class="reference internal" href="annotation_resources.html">Annotation resources</a></li>
+<li class="toctree-l1"><a class="reference internal" href="annotation_resources.html#notes-on-variant-annotation-datasets">Notes on variant annotation datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output.html">Input &amp; output</a></li>
 </ul>
 

docs/_build/html/_sources/annotation_resources.rst.txt

@@ -99,6 +99,11 @@
 <li class="toctree-l2"><a class="reference internal" href="#cancer-gene-knowledge-bases">Cancer gene knowledge bases</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="#notes-on-variant-annotation-datasets">Notes on variant annotation datasets</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#genome-mapping">Genome mapping</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#other-data-quality-concerns">Other data quality concerns</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="output.html">Input &amp; output</a></li>
 </ul>
 
@@ -223,6 +228,40 @@ <h2>Cancer gene knowledge bases<a class="headerlink" href="#cancer-gene-knowledg
 (February 2017)</li>
 </ul>
 </div>
+</div>
+<div class="section" id="notes-on-variant-annotation-datasets">
+<h1>Notes on variant annotation datasets<a class="headerlink" href="#notes-on-variant-annotation-datasets" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="genome-mapping">
+<h2>Genome mapping<a class="headerlink" href="#genome-mapping" title="Permalink to this headline">¶</a></h2>
+<p>A requirement for all variant annotation datasets used in PCGR is that
+they have been mapped unambiguously to the human genome (GRCh37). For
+most datasets this is already the case (i.e. dbSNP, COSMIC, ClinVar
+etc.). A significant proportion of variants in the annotation datasets
+related to clinical interpretation, CIViC and CBMDB, are however not
+mapped to the genome. Whenever possible, we have utilized
+<a class="reference external" href="http://bioinformatics.mdanderson.org/transvarweb/">TransVar</a> to
+identify the actual genomic variants (e.g. <em>g.chr7:140453136A&gt;T</em>) that
+corresponds to variants reported with other HGVS nomenclature (e.g.
+<em>p.V600E</em>).</p>
+</div>
+<div class="section" id="other-data-quality-concerns">
+<h2>Other data quality concerns<a class="headerlink" href="#other-data-quality-concerns" title="Permalink to this headline">¶</a></h2>
+<p><strong>Clinical biomarkers</strong> Clinical biomarkers included in PCGR is limited
+to the following: * Markers reported at the variant level (e.g. <strong>BRAF
+p.V600E</strong>) * Markers reported at the codon level (e.g. <strong>KRAS p.G12</strong>)
+* Markers reported at the exon level (e.g. <strong>KIT exon 11 mutation</strong>) *
+Within CBMDB, only markers collected from FDA/NCCN guidelines,
+scientific literature and clinical trials are included (markers
+collected from conference abstracts are not included)</p>
+<p><strong>COSMIC variants</strong> The COSMIC dataset that is part of the PCGR
+annotation bundle is the subset of variants that satisfy the following
+criteria: * <strong>Mutation somatic status</strong> is either
+&#8216;<em>confirmed_somatic</em>&#8216; or
+&#8216;<em>reported_in_another_cancer_sample_as_somatic</em>&#8216;. *
+<strong>Site/histology</strong> must be known and the sample must come from a
+malignant tumor (i.e. not polyps/adenomas, which are also found in
+COSMIC)</p>
+</div>
 </div>
 
 

docs/_build/html/_sources/getting_started.rst.txt

@@ -90,6 +90,7 @@
 <li class="toctree-l1"><a class="reference internal" href="about.html">About</a></li>
 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting started</a></li>
 <li class="toctree-l1"><a class="reference internal" href="annotation_resources.html">Annotation resources</a></li>
+<li class="toctree-l1"><a class="reference internal" href="annotation_resources.html#notes-on-variant-annotation-datasets">Notes on variant annotation datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output.html">Input &amp; output</a></li>
 </ul>
 

docs/_build/html/about.html

@@ -100,6 +100,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="annotation_resources.html">Annotation resources</a></li>
+<li class="toctree-l1"><a class="reference internal" href="annotation_resources.html#notes-on-variant-annotation-datasets">Notes on variant annotation datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="output.html">Input &amp; output</a></li>
 </ul>
 
@@ -195,7 +196,7 @@ <h3>Download PCGR<a class="headerlink" href="#download-pcgr" title="Permalink to
 <li><p class="first">Download and unpack the data bundle (approx. 17Gb) in the PCGR
 directory</p>
 <ul class="simple">
-<li>Download <a class="reference external" href="https://drive.google.com/file/d/0B8aYD2TJ472mRjkxMXVaNm1zQ1U/">the latest data
+<li>Download <a class="reference external" href="https://drive.google.com/file/d/0B8aYD2TJ472mQjZOMmg4djZfT1k/">the latest data
 bundle</a>
 from Google Drive to <code class="docutils literal"><span class="pre">~/pcgr-X.X</span></code> (replace <em>X.X</em> with the
 version number)</li>