diff --git a/README.md b/README.md
index 3abfbf16..fc18164a 100644
--- a/README.md
+++ b/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
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
index eea4cab9..1db5cb6a 100644
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diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
index 4f9b09b7..0d56aa1a 100644
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diff --git a/docs/_build/doctrees/output.doctree b/docs/_build/doctrees/output.doctree
index c214e788..3d9a5384 100644
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diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt
index 28f39266..0d0ec297 100644
--- a/docs/_build/html/_sources/getting_started.rst.txt
+++ b/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 `__ (3.2Gb) from
+ image `__ (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``
diff --git a/docs/_build/html/_sources/output.rst.txt b/docs/_build/html/_sources/output.rst.txt
index a83e3ae1..d52b9134 100644
--- a/docs/_build/html/_sources/output.rst.txt
+++ b/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 `__ is described within the
- `documentation page for
- vcfanno `__
+ alternative allele. This can be done with the help of either `vt
+ decompose `__ or
+ `vcflib's vcfbreakmulti `__.
+ 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 `__.
diff --git a/docs/_build/html/getting_started.html b/docs/_build/html/getting_started.html
index 362cd109..0bc4d2ba 100644
--- a/docs/_build/html/getting_started.html
+++ b/docs/_build/html/getting_started.html
@@ -182,9 +182,9 @@ Installation of Docker