0.5.1 release

README.md

@@ -8,14 +8,16 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 
 ### News
 
-* _November 14th 2017_: **0.5.0 release**
+* _November 14th 2017_: **0.5.1 release**
   * Updated version of VEP (v90)
   * Updated versions of ClinVar, Uniprot KB, CIViC, CBMDB
   * Removal of ExAC (replaced by gnomAD), removal of COSMIC due to licensing restrictions
   * Users can analyze samples run without matching control (i.e. tumor-only)
   * PCGR pipeline is now configured through a [TOML-based configuration file](https://github.com/toml-lang/toml)
   * Bug fixes / general speed improvements
-  * _Work in progress (0.5.1 release): Export of report data through JSON_
+  * _Work in progress: Export of report data through JSON_
+* _November 14th 2017_: **0.5.1 release**
+  * Bug fixing (VCF validation)
 
 ### Example reports
 * [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.0.pcgr.html)
@@ -30,7 +32,7 @@ If you use PCGR, please cite our preprint paper:
 
 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). bioRxiv. doi:[10.1101/122366](https://doi.org/10.1101/122366)
 
-### Annotation resources included in PCGR (v0.5.0)
+### Annotation resources included in PCGR (v0.5.1)
 
 * [VEP v90](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 90 (GENCODE v27 as the gene reference dataset)
 * [dBNSFP v3.4](https://sites.google.com/site/jpopgen/dbNSFP) - Database of non-synonymous functional predictions (March 2017)
@@ -71,14 +73,14 @@ A local installation of Python (it has been tested with [version 2.7.13](https:/
 
 #### STEP 2: Download PCGR
 
-1. Download and unpack the [latest software release (0.5.0)](https://github.com/sigven/pcgr/releases/latest)
+1. Download and unpack the [latest software release (0.5.1)](https://github.com/sigven/pcgr/releases/latest)
 2. Download and unpack the data bundle (approx. 16Gb) in the PCGR directory
-   * Download [the accompanying data bundle](https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g `~/pcgr-0.5.0`)
+   * Download [the accompanying data bundle](https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g `~/pcgr-0.5.1`)
    * 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
-3. Pull the [PCGR Docker image (0.5.0)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb):
-   * `docker pull sigven/pcgr:0.5.0` (PCGR annotation engine)
+3. Pull the [PCGR Docker image (0.5.1)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb):
+   * `docker pull sigven/pcgr:0.5.1` (PCGR annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -124,7 +126,7 @@ 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-0.5.0
+					e.g. ~/pcgr-0.5.1
 	output_dir            Output directory
 	configuration_file    PCGR configuration file (TOML format)
 	sample_id             Tumor sample/cancer genome identifier - prefix for
@@ -158,9 +160,9 @@ The configuration file, formatted using [TOML](https://github.com/toml-lang/toml
 
 The _examples_ folder contain input files from two tumor samples sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.0/examples/tumor_sample.COAD.vcf.gz`
-`--input_cna ~/pcgr-0.5.0/examples/tumor_sample.COAD.cna.tsv`
-` ~/pcgr-0.5.0/examples ~/pcgr-0.5.0/examples/pcgr_configuration.toml tumor_sample.COAD`
+`python pcgr.py --input_vcf ~/pcgr-0.5.1/examples/tumor_sample.COAD.vcf.gz`
+`--input_cna ~/pcgr-0.5.1/examples/tumor_sample.COAD.cna.tsv`
+` ~/pcgr-0.5.1/examples ~/pcgr-0.5.1/examples/pcgr_configuration.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/getting_started.rst.txt

@@ -55,15 +55,15 @@ Download PCGR
 ^^^^^^^^^^^^^
 
 -  Download and unpack the `latest software release
-   (0.5.0) <https://github.com/sigven/pcgr/releases/latest>`__
+   (0.5.1) <https://github.com/sigven/pcgr/releases/latest>`__
 
 -  Download and unpack the data bundle (approx. 16Gb) in the PCGR
    directory
 
    -  Download `the accompanying data
       bundle <https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/>`__
       from Google Drive to ``~/pcgr-X.X`` (replace *X.X* with the
-      version number, e.g. ``~/pcgr-0.5.0``)
+      version number, e.g. ``~/pcgr-0.5.1``)
    -  Decompress and untar the bundle, e.g. through the following Unix
       command:
       ``gzip -dc pcgr.databundle.GRCh37.YYYYMMDD.tgz | tar xvf -``
@@ -72,10 +72,10 @@ Download PCGR
    have been produced
 
 -  Pull the `PCGR Docker image -
-   0.5.0 <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
+   0.5.1 <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
    (approx 4.2Gb) :
 
-   -  ``docker pull sigven/pcgr:0.5.0`` (PCGR annotation engine)
+   -  ``docker pull sigven/pcgr:0.5.1`` (PCGR annotation engine)
 
 Run test - generation of clinical report for a cancer genome
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -94,7 +94,7 @@ 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-0.5.0
+                    e.g. ~/pcgr-0.5.1
     output_dir            Output directory
     configuration_file    PCGR configuration file (TOML format)
     sample_id             Tumor sample/cancer genome identifier - prefix for
@@ -135,9 +135,9 @@ sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.0/examples/tumor_sample.COAD.vcf.gz``
-``--input_cna ~/pcgr-0.5.0/examples/tumor_sample.COAD.cna.tsv``
-``~/pcgr-0.5.0/examples ~/pcgr-0.5.0/examples/pcgr_configuration.toml tumor_sample.COAD``
+``python pcgr.py --input_vcf ~/pcgr-0.5.1/examples/tumor_sample.COAD.vcf.gz``
+``--input_cna ~/pcgr-0.5.1/examples/tumor_sample.COAD.cna.tsv``
+``~/pcgr-0.5.1/examples ~/pcgr-0.5.1/examples/pcgr_configuration.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

@@ -482,29 +482,29 @@ processing with the PCGR annotation pipeline:
    mutations in
    cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
    database, as provided by VEP
--  *COSMIC\_CODON\_FRAC\_GW - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_CODON\_FRAC\_GW - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_CODON\_COUNT\_GW - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_CODON\_COUNT\_GW - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_SITE\_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_SITE\_HISTOLOGY - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_CANCER\_TYPE\_GW - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_CANCER\_TYPE\_GW - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_CANCER\_TYPE\_ALL - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_CANCER\_TYPE\_ALL - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_SITE\_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_SITE\_HISTOLOGY - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_CANCER\_TYPE\_GW - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_CANCER\_TYPE\_GW - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_SAMPLE\_SOURCE - Deprecated in 0.5.0 due to COSMIC licensing
+-  *COSMIC\_SAMPLE\_SOURCE - Deprecated in 0.5.1 due to COSMIC licensing
    restrictions*
--  *COSMIC\_DRUG\_RESISTANCE - Deprecated in 0.5.0 due to COSMIC
+-  *COSMIC\_DRUG\_RESISTANCE - Deprecated in 0.5.1 due to COSMIC
    licensing restrictions*
--  *COSMIC\_FATHMM\_PRED - Deprecated in 0.5.0 due to COSMIC licensing
+-  *COSMIC\_FATHMM\_PRED - Deprecated in 0.5.1 due to COSMIC licensing
    restrictions*
--  *COSMIC\_VARTYPE - Deprecated in 0.5.0 due to COSMIC licensing
+-  *COSMIC\_VARTYPE - Deprecated in 0.5.1 due to COSMIC licensing
    restrictions*
--  *COSMIC\_CONSEQUENCE - Deprecated in 0.5.0 due to COSMIC licensing
+-  *COSMIC\_CONSEQUENCE - Deprecated in 0.5.1 due to COSMIC licensing
    restrictions*
 
 .. raw:: html

docs/_build/html/getting_started.html

@@ -202,15 +202,15 @@ <h3>Python<a class="headerlink" href="#python" title="Permalink to this headline
 <h3>Download PCGR<a class="headerlink" href="#download-pcgr" title="Permalink to this headline">¶</a></h3>
 <ul>
 <li><p class="first">Download and unpack the <a class="reference external" href="https://github.com/sigven/pcgr/releases/latest">latest software release
-(0.5.0)</a></p>
+(0.5.1)</a></p>
 </li>
 <li><p class="first">Download and unpack the data bundle (approx. 16Gb) in the PCGR
 directory</p>
 <ul class="simple">
 <li>Download <a class="reference external" href="https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/">the accompanying 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, e.g. <code class="docutils literal"><span class="pre">~/pcgr-0.5.0</span></code>)</li>
+version number, e.g. <code class="docutils literal"><span class="pre">~/pcgr-0.5.1</span></code>)</li>
 <li>Decompress and untar the bundle, e.g. through the following Unix
 command:
 <code class="docutils literal"><span class="pre">gzip</span> <span class="pre">-dc</span> <span class="pre">pcgr.databundle.GRCh37.YYYYMMDD.tgz</span> <span class="pre">|</span> <span class="pre">tar</span> <span class="pre">xvf</span> <span class="pre">-</span></code></li>
@@ -219,10 +219,10 @@ <h3>Download PCGR<a class="headerlink" href="#download-pcgr" title="Permalink to
 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 -
-0.5.0</a> from DockerHub
+0.5.1</a> from DockerHub
 (approx 4.2Gb) :</p>
 <ul class="simple">
-<li><code class="docutils literal"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr:0.5.0</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:0.5.1</span></code> (PCGR annotation engine)</li>
 </ul>
 </li>
 </ul>
@@ -241,7 +241,7 @@ <h2>Run test - generation of clinical report for a cancer genome<a class="header
 
 <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">0.5</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">0.5</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="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>
 <span class="n">sample_id</span>             <span class="n">Tumor</span> <span class="n">sample</span><span class="o">/</span><span class="n">cancer</span> <span class="n">genome</span> <span class="n">identifier</span> <span class="o">-</span> <span class="n">prefix</span> <span class="k">for</span>
@@ -282,9 +282,9 @@ <h2>Run test - generation of clinical report for a cancer genome<a class="header
 sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.0/examples/tumor_sample.COAD.vcf.gz</span></code>
-<code class="docutils literal"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.5.0/examples/tumor_sample.COAD.cna.tsv</span></code>
-<code class="docutils literal"><span class="pre">~/pcgr-0.5.0/examples</span> <span class="pre">~/pcgr-0.5.0/examples/pcgr_configuration.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-0.5.1/examples/tumor_sample.COAD.vcf.gz</span></code>
+<code class="docutils literal"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.5.1/examples/tumor_sample.COAD.cna.tsv</span></code>
+<code class="docutils literal"><span class="pre">~/pcgr-0.5.1/examples</span> <span class="pre">~/pcgr-0.5.1/examples/pcgr_configuration.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/output.html

@@ -667,29 +667,29 @@ <h4><em>Variant frequencies/annotations in germline/somatic databases</em><a cla
 mutations in
 cancer</a>
 database, as provided by VEP</li>
-<li><em>COSMIC_CODON_FRAC_GW - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_CODON_FRAC_GW - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_CODON_COUNT_GW - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_CODON_COUNT_GW - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_CANCER_TYPE_ALL - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_CANCER_TYPE_ALL - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_SITE_HISTOLOGY - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_CANCER_TYPE_GW - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_SAMPLE_SOURCE - Deprecated in 0.5.0 due to COSMIC licensing
+<li><em>COSMIC_SAMPLE_SOURCE - Deprecated in 0.5.1 due to COSMIC licensing
 restrictions</em></li>
-<li><em>COSMIC_DRUG_RESISTANCE - Deprecated in 0.5.0 due to COSMIC
+<li><em>COSMIC_DRUG_RESISTANCE - Deprecated in 0.5.1 due to COSMIC
 licensing restrictions</em></li>
-<li><em>COSMIC_FATHMM_PRED - Deprecated in 0.5.0 due to COSMIC licensing
+<li><em>COSMIC_FATHMM_PRED - Deprecated in 0.5.1 due to COSMIC licensing
 restrictions</em></li>
-<li><em>COSMIC_VARTYPE - Deprecated in 0.5.0 due to COSMIC licensing
+<li><em>COSMIC_VARTYPE - Deprecated in 0.5.1 due to COSMIC licensing
 restrictions</em></li>
-<li><em>COSMIC_CONSEQUENCE - Deprecated in 0.5.0 due to COSMIC licensing
+<li><em>COSMIC_CONSEQUENCE - Deprecated in 0.5.1 due to COSMIC licensing
 restrictions</em></li>
 </ul>
 <!--- COSMIC\_MUTATION_ID - Mutation identifier in [Catalog of somatic mutations in cancer](http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/) database

docs/getting_started.md

@@ -27,16 +27,16 @@ An installation of Python (version 2.7.13) is required to run PCGR. Check that P
 
 #### Download PCGR
 
-* Download and unpack the [latest software release (0.5.0)](https://github.com/sigven/pcgr/releases/latest)
+* Download and unpack the [latest software release (0.5.1)](https://github.com/sigven/pcgr/releases/latest)
 
 * Download and unpack the data bundle (approx. 16Gb) in the PCGR directory
-    * Download [the accompanying data bundle](https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g. `~/pcgr-0.5.0`)
+    * Download [the accompanying data bundle](https://drive.google.com/file/d/1ZKDef-dsRA4rMv5jXU8vrBj5PvwOZ3vb/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g. `~/pcgr-0.5.1`)
     * Decompress and untar the 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
 
-* Pull the [PCGR Docker image - 0.5.0](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb) :
-    * `docker pull sigven/pcgr:0.5.0` (PCGR annotation engine)
+* Pull the [PCGR Docker image - 0.5.1](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb) :
+    * `docker pull sigven/pcgr:0.5.1` (PCGR annotation engine)
 
 
 ### Run test - generation of clinical report for a cancer genome
@@ -52,7 +52,7 @@ 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-0.5.0
+					e.g. ~/pcgr-0.5.1
 	output_dir            Output directory
 	configuration_file    PCGR configuration file (TOML format)
 	sample_id             Tumor sample/cancer genome identifier - prefix for
@@ -86,9 +86,9 @@ The configuration file, formatted using [TOML](https://github.com/toml-lang/toml
 
 The _examples_ folder contain input files from two tumor samples sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.0/examples/tumor_sample.COAD.vcf.gz`
-`--input_cna ~/pcgr-0.5.0/examples/tumor_sample.COAD.cna.tsv`
-` ~/pcgr-0.5.0/examples ~/pcgr-0.5.0/examples/pcgr_configuration.toml tumor_sample.COAD`
+`python pcgr.py --input_vcf ~/pcgr-0.5.1/examples/tumor_sample.COAD.vcf.gz`
+`--input_cna ~/pcgr-0.5.1/examples/tumor_sample.COAD.cna.tsv`
+` ~/pcgr-0.5.1/examples ~/pcgr-0.5.1/examples/pcgr_configuration.toml tumor_sample.COAD`
 
 This command will run the Docker-based PCGR workflow and produce the following output files in the _examples_ folder: