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OpenCRAVAT-Variant-Report.rst.old
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OpenCRAVAT-Variant-Report.rst.old
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==============
Variant Report
==============
OpenCRAVAT provides a whole-page variant report that describes an
individual variant. Try these examples below, which will open an
OpenCRAVAT Variant Report page from the OpenCRAVAT public server.
`OpenCRAVAT Variant Page example
1 <https://run.opencravat.org/webapps/variantreport/index.html?chrom=chr17&pos=39724004&ref_base=C&alt_base=G>`__
`OpenCRAVAT Variant Page example
2 <https://run.opencravat.org/webapps/variantreport/index.html?chrom=chr10&pos=87864470&ref_base=A&alt_base=T>`__
`OpenCRAVAT Variant Page example
3 <https://run.opencravat.org/webapps/variantreport/index.html?chrom=chr22&pos=19965038&ref_base=G&alt_base=A>`__
`OpenCRAVAT Variant Page example
4 <https://run.opencravat.org/webapps/variantreport/index.html?chrom=chr1&pos=1719358&ref_base=A&alt_base=G>`__
To enable OpenCRAVAT Variant Report pages in your own installation of
OpenCRAVAT, there are necessary annotation modules. Run the command
below to install the required modules.
::
oc module install lollipop hgvs chasmplus civic cosmic cgc cgl target gnomad thousandgenomes hgdp esp6500 abraom uk10k_cohort pharmgkb clinvar clingen denovo gwas_catalog ess_gene gnomad_gene prec phi ghis loftool interpro gtex rvis ncbigene vest mutpred1 mutation_assessor fathmm phdsnpg phastcons phylop linsight ncrna pseudogene biogrid intact ndex mupit
The OpenCRAVAT Variant Report page can be launched with the following
URL scheme:
::
http(s)://<OpenCRAVAT GUI domain>/result/nocache/variant.html?chrom=<chromosome>&pos=<genomic position>&ref_base=<reference base(s)>&alt_base=<alternate base(s)>
For example,
::
http://localhost:8060/result/nocache/variant.html?chrom=chr1&pos=12777320&ref_base=C&alt_base=T
If you open this URL the first time after starting ``oc gui``, the page
will take some time to load since the gene mapper and several required
annotators need to be loaded.
The Variant Report page has the following sections.
Variant Annotations
===================
.. figure:: figures/single-variant-report-variant-annotations.png
:alt: single variant report variant annotations
single variant report variant annotations
This section includes basic information on the input variant, the
mapping of the variant onto genes with variant consequences, mappings to
UniProt, HGVS notation of variant consequences, and a protein diagram
showing the location of the variant as well as Pfam and UniProt domain
annotations.
Cancer
======
.. figure:: figures/single-variant-report-cancer.png
:alt: single variant report cancer
single variant report cancer
Several cancer-related annotations are included in this section:
CHASMplus, CiVIC, COSMIC, Cancer Gene Census, Cancer Genome Landscape,
and TARGET.
Population Allele Frequencies
=============================
.. figure:: figures/single-variant-report-population-allele-frequencies.png
:alt: single variant report population allele frequencies
single variant report population allele frequencies
gnomAD, 1000 Genomes, HGDP, ESP6500, ABRaOM, and UK10K Cohorts allele
frequency annotations are shown in this section.
Clinical Relevance
==================
.. figure:: figures/single-variant-report-clinical-relevance.png
:alt: single variant report clinical relevance
single variant report clinical relevance
PharmGKB, ClinVar, ClinGen, denovo-db, and GWAS Catalog annotations are
shown in this section.
Gene
====
.. figure:: figures/single-variant-report-gene.png
:alt: single variant report gene
single variant report gene
Gene-level annotations are shown in this section: gnomAD Gene, P(rec),
P(HI), GHIS, LoFtool, RVIS, and NCBI Gene.
Pathogenicity Prediction
========================
.. figure:: figures/single-variant-report-pathogenicity-prediction.png
:alt: single variant report pathogenicity prediction
single variant report pathogenicity prediction
Several variant effect prediction annotations are included in this
section: VEST, PhDSNPg, MutPred, Mutation Assessor, and FATHMM.
Evolutionary Constraint
=======================
.. figure:: figures/single-variant-report-evolutionary-constraint.png
:alt: single variant report evolutionary constraint
single variant report evolutionary constraint
PhastCons and PhyloP annotations are shown in this section.
Noncoding and Genomic Elements
==============================
.. figure:: figures/single-variant-report-noncoding-and-genomic-elements.png
:alt: single variant report noncoding and genomic elements
single variant report noncoding and genomic elements
This section includes annotations from LINSIGHT, ncRNA, Pseudogene,
BioGRID, and IntAct.
Visualization
=============
.. figure:: figures/single-variant-report-visualization.png
:alt: single variant report visualization
single variant report visualization
NDEx and MuPIT visualizations are shown in this section. In the NDEx
visualization, use the dropdown menu to select different networks which
include the gene impacted by the variant. The variant's gene is shown in
red. In MuPIT visualization, click the triangle at the left bottom and
then click "Result" button to select different 3D protein structures to
which the variant was mapped. Also, click the triangle at the top right
to highlight TCGA mutations and UniProt-derived protein domains on the
shown 3D structure.