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61 changes: 30 additions & 31 deletions docs/_build/html/_sources/output.rst.txt
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Expand Up @@ -89,9 +89,11 @@ unique identifier of the tumor-normal sample pair to be analyzed.
- `View an example report for a colorectal tumor sample
(TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr.html>`__

The HTML reports have been tested using the following browsers: \*
Safari (10.0.3) \* Mozilla Firefox (52.0.2) \* Google Chrome
(57.0.2987.110)
The HTML reports have been tested using the following browsers:

- Safari (10.0.3)
- Mozilla Firefox (52.0.2)
- Google Chrome (57.0.2987.110)

Output - Somatic SNVs/InDels
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -374,51 +376,48 @@ processing with the PCGR annotation pipeline:
- GWAS\_CATALOG\_TRAIT\_URI - List of trait URIs for GWAS-associated
variant
- COSMIC\_MUTATION\_ID - Mutation identifier in `Catalog of somatic
mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
database
- COSMIC\_CODON\_FRAC\_GW - For different tumor types, number of
samples mutated at associated codon position (format:
codon\_number:tumor\_type:fraction\_mutated). Samples subject to
exome/genome-wide screens only `Catalog of somatic mutations in
cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_CODON\_COUNT\_GW - For different tumor types, number of
samples mutated at associated codon position (format:
codon\_number:tumor\_type:frequency). Samples subject to
exome/genome-wide screens only `Catalog of somatic mutations in
cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
- COSMIC\_COUNT\_GW - Global frequency of variant in `Catalog of
somatic mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
somatic mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_SITE\_HISTOLOGY - Primary site/histology distribution across
tumor types in `Catalog of somatic mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
tumor types in `Catalog of somatic mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_CANCER\_TYPE\_GW - Frequency of variant across different
tumor types in `Catalog of somatic mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__ -
samples subject to exome/genome-wide screens only
tumor types in `Catalog of somatic mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
- samples subject to exome/genome-wide screens only
- COSMIC\_CANCER\_TYPE\_ALL - Frequency of variant across different
tumor types in `Catalog of somatic mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
tumor types in `Catalog of somatic mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__
- COSMIC\_SAMPLE\_SOURCE - Sample source distribution for variant in
`Catalog of somatic mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
`Catalog of somatic mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_DRUG\_RESISTANCE - Targeted drugs/therapies subject to
resistance in tumors that carry the mutation. `Catalog of somatic
mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_FATHMM\_PRED - Variant effect prediction from COSMIC's FATHMM
algorithm (COSMIC variants only) `Catalog of somatic mutations in
cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_VARTYPE - COSMIC variant type `Catalog of somatic mutations
in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- COSMIC\_CONSEQUENCE - COSMIC consequence type `Catalog of somatic
mutations in cancer - COSMIC
v78 <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
mutations in
cancer <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>`__.
- ICGC\_PROJECTS - Variant frequency count in different `ICGC Project
IDs <https://dcc.icgc.org/repository/current/Projects>`__

Expand Down Expand Up @@ -527,7 +526,7 @@ The following variables are included in the tiered TSV file:
particular antineoplastic drug
28. CLINVAR - variant origin and associated traits associated with variant
29. CLINVAR_SIG - clinical significance of CLINVAR variant
30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC release 0.3.1
30. GLOBAL_AF_EXAC - adjusted global germline allele frequency in ExAC
31. GLOBAL_AF_1KG - 1000G Project - phase 3, germline allele frequency
for all 1000G project samples (global)
32. TIER
Expand Down Expand Up @@ -618,8 +617,8 @@ The format of the compressed TSV file is the following:
13. gene_biotype - type of gene
14. cancer_census_germline - gene implicated with germline predisposition to various cancer subtypes
15. cancer_census_somatic - gene for which somatic mutations have been causally implicated in tumor development
16. tsgene - tumor suppressor gene status (TSgene 2.0 database)
17. tsgene_oncogene - oncogene status (TSgene 2.0 database)
16. tsgene - tumor suppressor gene status (TSgene database)
17. tsgene_oncogene - oncogene status (TSgene database)
18. intogen_drivers - predicted driver gene status (IntoGen Cancer Drivers Database)
19. antineoplastic_drugs_dgidb - validated and experimental antineoplastic drugs interacting with gene
20. gencode_transcript_type -
Expand Down
62 changes: 31 additions & 31 deletions docs/_build/html/output.html
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Expand Up @@ -248,9 +248,12 @@ <h2>Output - Interactive HTML report<a class="headerlink" href="#output-interact
<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr.html">View an example report for a colorectal tumor sample
(TCGA)</a></li>
</ul>
<p>The HTML reports have been tested using the following browsers: *
Safari (10.0.3) * Mozilla Firefox (52.0.2) * Google Chrome
(57.0.2987.110)</p>
<p>The HTML reports have been tested using the following browsers:</p>
<ul class="simple">
<li>Safari (10.0.3)</li>
<li>Mozilla Firefox (52.0.2)</li>
<li>Google Chrome (57.0.2987.110)</li>
</ul>
</div>
<div class="section" id="output-somatic-snvs-indels">
<h2>Output - Somatic SNVs/InDels<a class="headerlink" href="#output-somatic-snvs-indels" title="Permalink to this headline"></a></h2>
Expand Down Expand Up @@ -532,51 +535,48 @@ <h4><em>Variant frequencies/annotations in germline/somatic databases</em><a cla
<li>GWAS_CATALOG_TRAIT_URI - List of trait URIs for GWAS-associated
variant</li>
<li>COSMIC_MUTATION_ID - Mutation identifier in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic
mutations in cancer - COSMIC
v78</a>
mutations in
cancer</a>
database</li>
<li>COSMIC_CODON_FRAC_GW - For different tumor types, number of
samples mutated at associated codon position (format:
codon_number:tumor_type:fraction_mutated). Samples subject to
exome/genome-wide screens only <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer - COSMIC
v78</a>.</li>
cancer</a>.</li>
<li>COSMIC_CODON_COUNT_GW - For different tumor types, number of
samples mutated at associated codon position (format:
codon_number:tumor_type:frequency). Samples subject to
exome/genome-wide screens only <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer - COSMIC
v78</a></li>
cancer</a></li>
<li>COSMIC_COUNT_GW - Global frequency of variant in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of
somatic mutations in cancer - COSMIC
v78</a>.</li>
somatic mutations in
cancer</a>.</li>
<li>COSMIC_SITE_HISTOLOGY - Primary site/histology distribution across
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in cancer - COSMIC
v78</a>.</li>
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer</a>.</li>
<li>COSMIC_CANCER_TYPE_GW - Frequency of variant across different
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in cancer - COSMIC
v78</a> -
samples subject to exome/genome-wide screens only</li>
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer</a>
- samples subject to exome/genome-wide screens only</li>
<li>COSMIC_CANCER_TYPE_ALL - Frequency of variant across different
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in cancer - COSMIC
v78</a></li>
tumor types in <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer</a></li>
<li>COSMIC_SAMPLE_SOURCE - Sample source distribution for variant in
<a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in cancer - COSMIC
v78</a>.</li>
<a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer</a>.</li>
<li>COSMIC_DRUG_RESISTANCE - Targeted drugs/therapies subject to
resistance in tumors that carry the mutation. <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic
mutations in cancer - COSMIC
v78</a>.</li>
mutations in
cancer</a>.</li>
<li>COSMIC_FATHMM_PRED - Variant effect prediction from COSMIC&#8217;s FATHMM
algorithm (COSMIC variants only) <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations in
cancer - COSMIC
v78</a>.</li>
cancer</a>.</li>
<li>COSMIC_VARTYPE - COSMIC variant type <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic mutations
in cancer - COSMIC
v78</a>.</li>
in
cancer</a>.</li>
<li>COSMIC_CONSEQUENCE - COSMIC consequence type <a class="reference external" href="http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/">Catalog of somatic
mutations in cancer - COSMIC
v78</a>.</li>
mutations in
cancer</a>.</li>
<li>ICGC_PROJECTS - Variant frequency count in different <a class="reference external" href="https://dcc.icgc.org/repository/current/Projects">ICGC Project
IDs</a></li>
</ul>
Expand Down Expand Up @@ -681,7 +681,7 @@ <h4>Annotated List of all SNVs/InDels<a class="headerlink" href="#annotated-list
<span class="n">particular</span> <span class="n">antineoplastic</span> <span class="n">drug</span>
<span class="mf">28.</span> <span class="n">CLINVAR</span> <span class="o">-</span> <span class="n">variant</span> <span class="n">origin</span> <span class="ow">and</span> <span class="n">associated</span> <span class="n">traits</span> <span class="n">associated</span> <span class="k">with</span> <span class="n">variant</span>
<span class="mf">29.</span> <span class="n">CLINVAR_SIG</span> <span class="o">-</span> <span class="n">clinical</span> <span class="n">significance</span> <span class="n">of</span> <span class="n">CLINVAR</span> <span class="n">variant</span>
<span class="mf">30.</span> <span class="n">GLOBAL_AF_EXAC</span> <span class="o">-</span> <span class="n">adjusted</span> <span class="k">global</span> <span class="n">germline</span> <span class="n">allele</span> <span class="n">frequency</span> <span class="ow">in</span> <span class="n">ExAC</span> <span class="n">release</span> <span class="mf">0.3</span><span class="o">.</span><span class="mi">1</span>
<span class="mf">30.</span> <span class="n">GLOBAL_AF_EXAC</span> <span class="o">-</span> <span class="n">adjusted</span> <span class="k">global</span> <span class="n">germline</span> <span class="n">allele</span> <span class="n">frequency</span> <span class="ow">in</span> <span class="n">ExAC</span>
<span class="mf">31.</span> <span class="n">GLOBAL_AF_1KG</span> <span class="o">-</span> <span class="mi">1000</span><span class="n">G</span> <span class="n">Project</span> <span class="o">-</span> <span class="n">phase</span> <span class="mi">3</span><span class="p">,</span> <span class="n">germline</span> <span class="n">allele</span> <span class="n">frequency</span>
<span class="k">for</span> <span class="nb">all</span> <span class="mi">1000</span><span class="n">G</span> <span class="n">project</span> <span class="n">samples</span> <span class="p">(</span><span class="k">global</span><span class="p">)</span>
<span class="mf">32.</span> <span class="n">TIER</span>
Expand Down Expand Up @@ -761,8 +761,8 @@ <h3>1. Tab-separated values (TSV)<a class="headerlink" href="#id1" title="Permal
<span class="mf">13.</span> <span class="n">gene_biotype</span> <span class="o">-</span> <span class="nb">type</span> <span class="n">of</span> <span class="n">gene</span>
<span class="mf">14.</span> <span class="n">cancer_census_germline</span> <span class="o">-</span> <span class="n">gene</span> <span class="n">implicated</span> <span class="k">with</span> <span class="n">germline</span> <span class="n">predisposition</span> <span class="n">to</span> <span class="n">various</span> <span class="n">cancer</span> <span class="n">subtypes</span>
<span class="mf">15.</span> <span class="n">cancer_census_somatic</span> <span class="o">-</span> <span class="n">gene</span> <span class="k">for</span> <span class="n">which</span> <span class="n">somatic</span> <span class="n">mutations</span> <span class="n">have</span> <span class="n">been</span> <span class="n">causally</span> <span class="n">implicated</span> <span class="ow">in</span> <span class="n">tumor</span> <span class="n">development</span>
<span class="mf">16.</span> <span class="n">tsgene</span> <span class="o">-</span> <span class="n">tumor</span> <span class="n">suppressor</span> <span class="n">gene</span> <span class="n">status</span> <span class="p">(</span><span class="n">TSgene</span> <span class="mf">2.0</span> <span class="n">database</span><span class="p">)</span>
<span class="mf">17.</span> <span class="n">tsgene_oncogene</span> <span class="o">-</span> <span class="n">oncogene</span> <span class="n">status</span> <span class="p">(</span><span class="n">TSgene</span> <span class="mf">2.0</span> <span class="n">database</span><span class="p">)</span>
<span class="mf">16.</span> <span class="n">tsgene</span> <span class="o">-</span> <span class="n">tumor</span> <span class="n">suppressor</span> <span class="n">gene</span> <span class="n">status</span> <span class="p">(</span><span class="n">TSgene</span> <span class="n">database</span><span class="p">)</span>
<span class="mf">17.</span> <span class="n">tsgene_oncogene</span> <span class="o">-</span> <span class="n">oncogene</span> <span class="n">status</span> <span class="p">(</span><span class="n">TSgene</span> <span class="n">database</span><span class="p">)</span>
<span class="mf">18.</span> <span class="n">intogen_drivers</span> <span class="o">-</span> <span class="n">predicted</span> <span class="n">driver</span> <span class="n">gene</span> <span class="n">status</span> <span class="p">(</span><span class="n">IntoGen</span> <span class="n">Cancer</span> <span class="n">Drivers</span> <span class="n">Database</span><span class="p">)</span>
<span class="mf">19.</span> <span class="n">antineoplastic_drugs_dgidb</span> <span class="o">-</span> <span class="n">validated</span> <span class="ow">and</span> <span class="n">experimental</span> <span class="n">antineoplastic</span> <span class="n">drugs</span> <span class="n">interacting</span> <span class="k">with</span> <span class="n">gene</span>
<span class="mf">20.</span> <span class="n">gencode_transcript_type</span> <span class="o">-</span>
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