0.6.1 fix

README.md

@@ -7,6 +7,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 ![PCGR overview](PCGR_workflow.png)
 
 ### News
+* _May 2nd 2018_: **0.6.1 release**
+   * Fixed bugs in tier assignment
 * _April 25th 2018_: **0.6.0 release**
    * Updated data sources
    * Enabling specification of tumor type of input sample
@@ -32,8 +34,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 
 
 ### Example reports
-* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.0.html)
-* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.0.html)
+* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.1.html)
+* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.1.html)
 
 
 ### PCGR documentation
@@ -44,7 +46,7 @@ If you use PCGR, please cite our recent publication:
 
 Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. __Personal Cancer Genome Reporter: variant interpretation report for precision oncology__ (2017). _Bioinformatics (in press)_. doi:[10.1093/bioinformatics/btx817](https://doi.org/10.1093/bioinformatics/btx817)
 
-### Annotation resources included in PCGR (0.6.0)
+### Annotation resources included in PCGR (0.6.1)
 
 * [VEP v92](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 92 (GENCODE v28/v19 as the gene reference dataset)
 * [CIViC](http://civic.genome.wustl.edu) - Clinical interpretations of variants in cancer (April 16th 2018)
@@ -83,15 +85,15 @@ An installation of Python (version _3.6_) is required to run PCGR. Check that Py
 
 #### STEP 2: Download PCGR and data bundle
 
-1. Download and unpack the [latest software release (0.6.0)](https://github.com/sigven/pcgr/releases/tag/v0.6.0)
+1. Download and unpack the [latest software release (0.6.1)](https://github.com/sigven/pcgr/releases/tag/v0.6.1)
 2. Download and unpack the assembly-specific data bundle in the PCGR directory
    * [grch37 data bundle](https://drive.google.com/open?id=1tOyPmzgXkSZjPJQOojFQxUP8JlQuQqLq) (approx 9Gb)
    * [grch38 data bundle](https://drive.google.com/open?id=1cKq-rgSNCYPCUJ38pCi_xy6_PJH-FZWD) (approx 9Gb)
    * *Unpacking*: `gzip -dc pcgr.databundle.grch37.YYYYMMDD.tgz | tar xvf -`
 
     A _data/_ folder within the _pcgr-X.X_ software folder should now have been produced
-3. Pull the [PCGR Docker image (0.6.0)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb):
-   * `docker pull sigven/pcgr:0.6.0` (PCGR annotation engine)
+3. Pull the [PCGR Docker image (0.6.1)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb):
+   * `docker pull sigven/pcgr:0.6.1` (PCGR annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -134,7 +136,9 @@ The PCGR configuration file, formatted using [TOML](https://github.com/toml-lang
 * VEP/_vcfanno_ options
 * Log-ratio thresholds for gains/losses in CNA analysis
 
-See here for more details about the exact [usage of the configuration options](http://pcgr.readthedocs.io/en/latest/input.html#PCGR-configuration-file)
+See here for more details about the exact [usage of the configuration options](http://pcgr.readthedocs.io/en/latest/input.html#pcgr-configuration-file).
+
+The PCGR software bundle comes with a default configuration file (*pcgr.toml*), to be used as a starting point for runnning the PCGR workflow.
 
 #### STEP 5: Run example
 
@@ -150,7 +154,7 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi
 
 	positional arguments:
 	pcgr_dir              PCGR base directory with accompanying data directory,
-				    e.g. ~/pcgr-0.6.0
+				    e.g. ~/pcgr-0.6.1
 	output_dir            Output directory
 	{grch37,grch38}       Genome assembly build: grch37 or grch38
 	configuration_file    PCGR configuration file (TOML format)
@@ -177,11 +181,11 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi
 
 
 
-The _examples_ folder contain input files from two tumor samples sequenced within TCGA. It also contains PCGR configuration files. A report for a colorectal tumor case can be generated by running the following command in your terminal window:
+The _examples_ folder contain input files from two tumor samples sequenced within TCGA (**GRCh37** only). It also contains PCGR configuration files customized for these cases. A report for a colorectal tumor case can be generated by running the following command in your terminal window:
 
-`python pcgr.py --input_vcf ~/pcgr-0.6.0/examples/tumor_sample.COAD.vcf.gz`
-`--input_cna ~/pcgr-0.6.0/examples/tumor_sample.COAD.cna.tsv`
-` ~/pcgr-0.6.0 ~/pcgr-0.6.0/examples grch37 ~/pcgr-0.6.0/examples/pcgr_conf.COAD.toml tumor_sample.COAD`
+`python pcgr.py --input_vcf ~/pcgr-0.6.1/examples/tumor_sample.COAD.vcf.gz`
+`--input_cna ~/pcgr-0.6.1/examples/tumor_sample.COAD.cna.tsv`
+` ~/pcgr-0.6.1 ~/pcgr-0.6.1/examples grch37 ~/pcgr-0.6.1/examples/pcgr_conf.COAD.toml tumor_sample.COAD`
 
 
 This command will run the Docker-based PCGR workflow and produce the following output files in the _examples_ folder:

docs/_build/html/CHANGELOG.html

@@ -94,6 +94,10 @@
 <li class="toctree-l1"><a class="reference internal" href="output.html">Output</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tier_systems.html">Tier models</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">CHANGELOG</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#may-2nd-2018">0.6.1 - May 2nd 2018</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#fixed">Fixed</a></li>
+</ul>
+</li>
 <li class="toctree-l2"><a class="reference internal" href="#april-25th-2018">0.6.0 - April 25th 2018</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#added">Added</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#removed">Removed</a></li>
@@ -148,6 +152,23 @@
 
   <div class="section" id="changelog">
 <h1>CHANGELOG<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="may-2nd-2018">
+<h2>0.6.1 - May 2nd 2018<a class="headerlink" href="#may-2nd-2018" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="fixed">
+<h3>Fixed<a class="headerlink" href="#fixed" title="Permalink to this headline">¶</a></h3>
+<ul class="simple">
+<li>Bug in tier assignment &#8216;pcgr_acmg&#8217; (case for no variants in
+tier1,2,3)</li>
+<li>Bug in tier assignment &#8216;pcgr_acmg&#8217; (no tumor type specified,
+evidence items with weak support detected)</li>
+<li>Bug: duplicated variants in &#8216;Tier 3&#8217; resulting from genes encoded
+with dual roles as tumor suppressor genes/oncogenes</li>
+<li>Bug: duplicated variants in &#8216;Tier 1/Noncoding variants&#8217; resulting
+from rare cases of noncoding variants occurring in Tier 1 (synonymous
+variants with biomarker role)</li>
+</ul>
+</div>
+</div>
 <div class="section" id="april-25th-2018">
 <h2>0.6.0 - April 25th 2018<a class="headerlink" href="#april-25th-2018" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="added">

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

@@ -1,6 +1,22 @@
 CHANGELOG
 ---------
 
+0.6.1 - May 2nd 2018
+^^^^^^^^^^^^^^^^^^^^
+
+Fixed
+'''''
+
+-  Bug in tier assignment 'pcgr\_acmg' (case for no variants in
+   tier1,2,3)
+-  Bug in tier assignment 'pcgr\_acmg' (no tumor type specified,
+   evidence items with weak support detected)
+-  Bug: duplicated variants in 'Tier 3' resulting from genes encoded
+   with dual roles as tumor suppressor genes/oncogenes
+-  Bug: duplicated variants in 'Tier 1/Noncoding variants' resulting
+   from rare cases of noncoding variants occurring in Tier 1 (synonymous
+   variants with biomarker role)
+
 0.6.0 - April 25th 2018
 ^^^^^^^^^^^^^^^^^^^^^^^
 

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

@@ -26,9 +26,9 @@ Example reports
 ~~~~~~~~~~~~~~~
 
 -  `Report for a breast tumor sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.0.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.1.html>`__
 -  `Report for a colon adenocarcinoma sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.0.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.1.html>`__
 
 Why use PCGR?
 ~~~~~~~~~~~~~

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

@@ -45,7 +45,7 @@ STEP 2: Download PCGR and data bundle
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 1. Download and unpack the `latest software release
-   (0.6.0) <https://github.com/sigven/pcgr/releases/tag/v0.6.0>`__
+   (0.6.1) <https://github.com/sigven/pcgr/releases/tag/v0.6.1>`__
 2. Download and unpack the assembly-specific data bundle in the PCGR
    directory
 
@@ -61,10 +61,10 @@ STEP 2: Download PCGR and data bundle
    A *data/* folder within the *pcgr-X.X* software folder should now
    have been produced
 3. Pull the `PCGR Docker image
-   (0.6.0) <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
+   (0.6.1) <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
    (approx 5.1Gb):
 
-   -  ``docker pull sigven/pcgr:0.6.0`` (PCGR annotation engine)
+   -  ``docker pull sigven/pcgr:0.6.1`` (PCGR annotation engine)
 
 STEP 3: Input preprocessing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -146,7 +146,7 @@ A tumor sample report is generated by calling the Python script
 
     positional arguments:
     pcgr_dir              PCGR base directory with accompanying data directory,
-                    e.g. ~/pcgr-0.6.0
+                    e.g. ~/pcgr-0.6.1
     output_dir            Output directory
     {grch37,grch38}       Genome assembly build: grch37 or grch38
     configuration_file    PCGR configuration file (TOML format)
@@ -175,9 +175,9 @@ sequenced within TCGA. It also contains PCGR configuration files. A
 report for a colorectal tumor case can be generated by running the
 following command in your terminal window:
 
-``python pcgr.py --input_vcf ~/pcgr-0.6.0/examples/tumor_sample.COAD.vcf.gz``
-``--input_cna ~/pcgr-0.6.0/examples/tumor_sample.COAD.cna.tsv``
-``~/pcgr-0.6.0 ~/pcgr-0.6.0/examples grch37 ~/pcgr-0.6.0/examples/pcgr_conf.COAD.toml tumor_sample.COAD``
+``python pcgr.py --input_vcf ~/pcgr-0.6.1/examples/tumor_sample.COAD.vcf.gz``
+``--input_cna ~/pcgr-0.6.1/examples/tumor_sample.COAD.cna.tsv``
+``~/pcgr-0.6.1 ~/pcgr-0.6.1/examples grch37 ~/pcgr-0.6.1/examples/pcgr_conf.COAD.toml tumor_sample.COAD``
 
 This command will run the Docker-based PCGR workflow and produce the
 following output files in the *examples* folder:

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

@@ -217,9 +217,9 @@ following:
 Example reports:
 
 -  `View an example report for a breast tumor sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.0.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.1.html>`__
 -  `View an example report for a colon adenocarcinoma sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.0.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.1.html>`__
 
 The HTML reports have been tested using the following browsers:
 

docs/_build/html/about.html

@@ -170,9 +170,9 @@ <h2>What is the Personal Cancer Genome Reporter (PCGR)?<a class="headerlink" hre
 <div class="section" id="example-reports">
 <h2>Example reports<a class="headerlink" href="#example-reports" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.0.html">Report for a breast tumor sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.1.html">Report for a breast tumor sample
 (TCGA)</a></li>
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.0.html">Report for a colon adenocarcinoma sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.1.html">Report for a colon adenocarcinoma sample
 (TCGA)</a></li>
 </ul>
 </div>

docs/_build/html/getting_started.html

@@ -192,8 +192,8 @@ <h2>STEP 1: Installation of Docker<a class="headerlink" href="#step-1-installati
 <div class="section" id="step-2-download-pcgr-and-data-bundle">
 <h2>STEP 2: Download PCGR and data bundle<a class="headerlink" href="#step-2-download-pcgr-and-data-bundle" title="Permalink to this headline">¶</a></h2>
 <ol class="arabic">
-<li><p class="first">Download and unpack the <a class="reference external" href="https://github.com/sigven/pcgr/releases/tag/v0.6.0">latest software release
-(0.6.0)</a></p>
+<li><p class="first">Download and unpack the <a class="reference external" href="https://github.com/sigven/pcgr/releases/tag/v0.6.1">latest software release
+(0.6.1)</a></p>
 </li>
 <li><p class="first">Download and unpack the assembly-specific data bundle in the PCGR
 directory</p>
@@ -211,10 +211,10 @@ <h2>STEP 2: Download PCGR and data bundle<a class="headerlink" href="#step-2-dow
 have been produced</p>
 </li>
 <li><p class="first">Pull the <a class="reference external" href="https://hub.docker.com/r/sigven/pcgr/">PCGR Docker image
-(0.6.0)</a> from DockerHub
+(0.6.1)</a> from DockerHub
 (approx 5.1Gb):</p>
 <ul class="simple">
-<li><code class="docutils literal"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr:0.6.0</span></code> (PCGR annotation engine)</li>
+<li><code class="docutils literal"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr:0.6.1</span></code> (PCGR annotation engine)</li>
 </ul>
 </li>
 </ol>
@@ -292,7 +292,7 @@ <h2>STEP 5: Run example<a class="headerlink" href="#step-5-run-example" title="P
 
 <span class="n">positional</span> <span class="n">arguments</span><span class="p">:</span>
 <span class="n">pcgr_dir</span>              <span class="n">PCGR</span> <span class="n">base</span> <span class="n">directory</span> <span class="k">with</span> <span class="n">accompanying</span> <span class="n">data</span> <span class="n">directory</span><span class="p">,</span>
-                <span class="n">e</span><span class="o">.</span><span class="n">g</span><span class="o">.</span> <span class="o">~/</span><span class="n">pcgr</span><span class="o">-</span><span class="mf">0.6</span><span class="o">.</span><span class="mi">0</span>
+                <span class="n">e</span><span class="o">.</span><span class="n">g</span><span class="o">.</span> <span class="o">~/</span><span class="n">pcgr</span><span class="o">-</span><span class="mf">0.6</span><span class="o">.</span><span class="mi">1</span>
 <span class="n">output_dir</span>            <span class="n">Output</span> <span class="n">directory</span>
 <span class="p">{</span><span class="n">grch37</span><span class="p">,</span><span class="n">grch38</span><span class="p">}</span>       <span class="n">Genome</span> <span class="n">assembly</span> <span class="n">build</span><span class="p">:</span> <span class="n">grch37</span> <span class="ow">or</span> <span class="n">grch38</span>
 <span class="n">configuration_file</span>    <span class="n">PCGR</span> <span class="n">configuration</span> <span class="n">file</span> <span class="p">(</span><span class="n">TOML</span> <span class="nb">format</span><span class="p">)</span>
@@ -321,9 +321,9 @@ <h2>STEP 5: Run example<a class="headerlink" href="#step-5-run-example" title="P
 sequenced within TCGA. It also contains PCGR configuration files. A
 report for a colorectal tumor case can be generated by running the
 following command in your terminal window:</p>
-<p><code class="docutils literal"><span class="pre">python</span> <span class="pre">pcgr.py</span> <span class="pre">--input_vcf</span> <span class="pre">~/pcgr-0.6.0/examples/tumor_sample.COAD.vcf.gz</span></code>
-<code class="docutils literal"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.6.0/examples/tumor_sample.COAD.cna.tsv</span></code>
-<code class="docutils literal"><span class="pre">~/pcgr-0.6.0</span> <span class="pre">~/pcgr-0.6.0/examples</span> <span class="pre">grch37</span> <span class="pre">~/pcgr-0.6.0/examples/pcgr_conf.COAD.toml</span> <span class="pre">tumor_sample.COAD</span></code></p>
+<p><code class="docutils literal"><span class="pre">python</span> <span class="pre">pcgr.py</span> <span class="pre">--input_vcf</span> <span class="pre">~/pcgr-0.6.1/examples/tumor_sample.COAD.vcf.gz</span></code>
+<code class="docutils literal"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.6.1/examples/tumor_sample.COAD.cna.tsv</span></code>
+<code class="docutils literal"><span class="pre">~/pcgr-0.6.1</span> <span class="pre">~/pcgr-0.6.1/examples</span> <span class="pre">grch37</span> <span class="pre">~/pcgr-0.6.1/examples/pcgr_conf.COAD.toml</span> <span class="pre">tumor_sample.COAD</span></code></p>
 <p>This command will run the Docker-based PCGR workflow and produce the
 following output files in the <em>examples</em> folder:</p>
 <ol class="arabic simple">

docs/_build/html/index.html

@@ -190,6 +190,7 @@ <h1>Welcome to Personal Cancer Genome Reporter&#8217;s documentation!<a class="h
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="CHANGELOG.html">CHANGELOG</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#may-2nd-2018">0.6.1 - May 2nd 2018</a></li>
 <li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#april-25th-2018">0.6.0 - April 25th 2018</a></li>
 </ul>
 </li>

docs/_build/html/output.html

@@ -385,9 +385,9 @@ <h3>Interactive datatables<a class="headerlink" href="#interactive-datatables" t
 </ul>
 <p>Example reports:</p>
 <ul class="simple">
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.0.html">View an example report for a breast tumor sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.0.6.1.html">View an example report for a breast tumor sample
 (TCGA)</a></li>
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.0.html">View an example report for a colon adenocarcinoma sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.0.6.1.html">View an example report for a colon adenocarcinoma sample
 (TCGA)</a></li>
 </ul>
 <p>The HTML reports have been tested using the following browsers:</p>