update docs

README.md

@@ -40,7 +40,7 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package int
 
 #### STEP 0: Python
 
-An installation of Python ([version 2.7.10 or higher](https://www.python.org/downloads/) is required to run PCGR. Check that Python is installed by typing `python --version` in a terminal window.
+A local installation of Python (it has been tested with [version 2.7.13](https://www.python.org/downloads/)) is required to run PCGR. Check that Python is installed by typing `python --version` in a terminal window.
 
 #### STEP 1: Installation of Docker
 
@@ -66,14 +66,14 @@ An installation of Python ([version 2.7.10 or higher](https://www.python.org/dow
 
 The PCGR workflow accepts two types of input files:
 
-  * An unannotated, single-sample VCF file with called somatic variants (SNVs/InDels)
+  * An unannotated, single-sample VCF file (>= v4.2) with called somatic variants (SNVs/InDels)
   * A copy number segment file
 
 PCGR can be run with either or both of the two input files present.
 
 The following requirements __MUST__ be met by the input VCF for PCGR to work properly:
 
-1. Variants in the raw VCF that contain multiple alternative alleles (e.g. "multiple ALTs") must be split into variants with a single alternative allele. A description on how this can be done with the help of [vt](https://github.com/atks/vt) is described within the [documentation page for vcfanno](http://brentp.github.io/vcfanno/#preprocessing)
+1. Variants in the raw VCF that contain multiple alternative alleles (e.g. "multiple ALTs") must be split into variants with a single alternative allele. This can be done with the help of either [vt decompose](http://genome.sph.umich.edu/wiki/Vt#Decompose) or [vcflib's vcfbreakmulti](https://github.com/vcflib/vcflib#vcflib). We will add integrated support for this in an upcoming release
 2. The contents of the VCF must be sorted correctly (i.e. according to chromosomal order and chromosomal position). This can be obtained by [vcftools](https://vcftools.github.io/perl_module.html#vcf-sort).
    * We strongly recommend that the input VCF is compressed and indexed using [bgzip](http://www.htslib.org/doc/tabix.html) and [tabix](http://www.htslib.org/doc/tabix.html)
    * 'chr' must be stripped from the chromosome names

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

@@ -35,9 +35,9 @@ Installation of Docker
 Python
 ^^^^^^
 
-An installation of Python (version 2.7.10 or higher) is required to run
-PCGR. Check that Python is installed by typing ``python --version`` in
-your terminal window.
+An installation of Python (version 2.7.13) is required to run PCGR.
+Check that Python is installed by typing ``python --version`` in your
+terminal window.
 
 Download PCGR
 ^^^^^^^^^^^^^
@@ -60,7 +60,7 @@ Download PCGR
    have been produced
 
 -  Pull the `PCGR Docker
-   image <https://hub.docker.com/r/sigven/pcgr/>`__ (3.2Gb) from
+   image <https://hub.docker.com/r/sigven/pcgr/>`__ (3.5Gb) from
    DockerHub):
 
    -  ``docker pull sigven/pcgr`` (PCGR annotation engine)
@@ -115,8 +115,9 @@ A tumor sample report is generated by calling the Python script
                         overwrite of existing result files by using this flag
                         (default: False)
 
-The *examples* folder contain sample files from TCGA. A report for a
-colorectal tumor case can be generated through the following command:
+The *examples* folder contain input files from two tumor samples
+sequenced within TCGA. A report for a colorectal tumor case can be
+generated by running the following command in your terminal window:
 
 ``python run_pcgr.py --input_vcf tumor_sample.COAD.vcf.gz --input_cna_segments``
 ``tumor_sample.COAD.cna.tsv ~/pcgr-X.X ~/pcgr-X.X/examples tumor_sample.COAD``

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

@@ -6,8 +6,8 @@ Input
 
 The PCGR workflow accepts two types of input files:
 
--  An unannotated, single-sample VCF file with called somatic variants
-   (SNVs/InDels)
+-  An unannotated, single-sample VCF file (>= v4.2) with called somatic
+   variants (SNVs/InDels)
 -  A copy number segment file
 
 PCGR can be run with either or both of the two input files present.
@@ -23,10 +23,10 @@ work properly:
 
 1. Variants in the raw VCF that contain multiple alternative alleles
    (e.g. "multiple ALTs") must be split into variants with a single
-   alternative allele. A description on how this can be done with the
-   help of `vt <https://github.com/atks/vt>`__ is described within the
-   `documentation page for
-   vcfanno <http://brentp.github.io/vcfanno/#preprocessing>`__
+   alternative allele. This can be done with the help of either `vt
+   decompose <http://genome.sph.umich.edu/wiki/Vt#Decompose>`__ or
+   `vcflib's vcfbreakmulti <https://github.com/vcflib/vcflib#vcflib>`__.
+   We will add integrated support for this in an upcoming release
 2. The contents of the VCF must be sorted correctly (i.e. according to
    chromosomal order and chromosomal position). This can be obtained by
    `vcftools <https://vcftools.github.io/perl_module.html#vcf-sort>`__.

docs/_build/html/getting_started.html

@@ -182,9 +182,9 @@ <h3>Installation of Docker<a class="headerlink" href="#installation-of-docker" t
 </div>
 <div class="section" id="python">
 <h3>Python<a class="headerlink" href="#python" title="Permalink to this headline">¶</a></h3>
-<p>An installation of Python (version 2.7.10 or higher) is required to run
-PCGR. Check that Python is installed by typing <code class="docutils literal"><span class="pre">python</span> <span class="pre">--version</span></code> in
-your terminal window.</p>
+<p>An installation of Python (version 2.7.13) is required to run PCGR.
+Check that Python is installed by typing <code class="docutils literal"><span class="pre">python</span> <span class="pre">--version</span></code> in your
+terminal window.</p>
 </div>
 <div class="section" id="download-pcgr">
 <h3>Download PCGR<a class="headerlink" href="#download-pcgr" title="Permalink to this headline">¶</a></h3>
@@ -207,7 +207,7 @@ <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</a> (3.2Gb) from
+image</a> (3.5Gb) from
 DockerHub):</p>
 <ul class="simple">
 <li><code class="docutils literal"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr</span></code> (PCGR annotation engine)</li>
@@ -263,8 +263,9 @@ <h2>Run test - generation of clinical report for a cancer genome<a class="header
                     <span class="p">(</span><span class="n">default</span><span class="p">:</span> <span class="kc">False</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>The <em>examples</em> folder contain sample files from TCGA. A report for a
-colorectal tumor case can be generated through the following command:</p>
+<p>The <em>examples</em> folder contain input files from two tumor samples
+sequenced within TCGA. 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">run_pcgr.py</span> <span class="pre">--input_vcf</span> <span class="pre">tumor_sample.COAD.vcf.gz</span> <span class="pre">--input_cna_segments</span></code>
 <code class="docutils literal"><span class="pre">tumor_sample.COAD.cna.tsv</span> <span class="pre">~/pcgr-X.X</span> <span class="pre">~/pcgr-X.X/examples</span> <span class="pre">tumor_sample.COAD</span></code></p>
 <p>This command will run the Docker-based PCGR workflow and produce the

docs/_build/html/output.html

@@ -171,8 +171,8 @@ <h1>Input &amp; output<a class="headerlink" href="#input-output" title="Permalin
 <h2>Input<a class="headerlink" href="#input" title="Permalink to this headline">¶</a></h2>
 <p>The PCGR workflow accepts two types of input files:</p>
 <ul class="simple">
-<li>An unannotated, single-sample VCF file with called somatic variants
-(SNVs/InDels)</li>
+<li>An unannotated, single-sample VCF file (&gt;= v4.2) with called somatic
+variants (SNVs/InDels)</li>
 <li>A copy number segment file</li>
 </ul>
 <p>PCGR can be run with either or both of the two input files present.</p>
@@ -185,10 +185,10 @@ <h3>VCF<a class="headerlink" href="#vcf" title="Permalink to this headline">¶</
 <ol class="arabic simple">
 <li>Variants in the raw VCF that contain multiple alternative alleles
 (e.g. &#8220;multiple ALTs&#8221;) must be split into variants with a single
-alternative allele. A description on how this can be done with the
-help of <a class="reference external" href="https://github.com/atks/vt">vt</a> is described within the
-<a class="reference external" href="http://brentp.github.io/vcfanno/#preprocessing">documentation page for
-vcfanno</a></li>
+alternative allele. This can be done with the help of either <a class="reference external" href="http://genome.sph.umich.edu/wiki/Vt#Decompose">vt
+decompose</a> or
+<a class="reference external" href="https://github.com/vcflib/vcflib#vcflib">vcflib&#8217;s vcfbreakmulti</a>.
+We will add integrated support for this in an upcoming release</li>
 <li>The contents of the VCF must be sorted correctly (i.e. according to
 chromosomal order and chromosomal position). This can be obtained by
 <a class="reference external" href="https://vcftools.github.io/perl_module.html#vcf-sort">vcftools</a>.<ul>