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diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md
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 # Table of contents
 
 * [README](README.md)
+* [Overview](overview.md)
+* [Installation](installation.md)
+
+## User Manuals
+
+* [IVA General Usage](user-manuals/iva-general-usage.md)
+* [Variant Browser](user-manuals/variant-browser.md)
+* [Case Interpreter](user-manuals/case-interpreter.md)
+* [Variant Analysis](user-manuals/variant-analysis.md)
+* [Catalog Browser](user-manuals/catalog-browser.md)
 
diff --git a/docs/installation.md b/docs/installation.md
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+# Installation
+
+## Quick installation
+
+### Bare installation
+
+* Download the latest tar.gz package from [https://github.com/opencb/iva/releases](https://github.com/opencb/iva/releases).
+* Extract the package `tar -xvf iva-[VERSION].tar.gz`
+* Move the folder into the working directory of a static web server of your choice \(e.g. Apache\)
+
+### Docker
+
+IVA is also provided as a Docker image here [https://hub.docker.com/repository/docker/opencb/iva-app](https://hub.docker.com/repository/docker/opencb/iva-app).  
+
+Pull and lauch the container:  
+`docker run --rm --name iva -p 8000:80 opencb/iva-app`
+
+Then visit:  
+`localhost:8000/iva`
+
+## Installation for developers
+
+### Clone
+
+The repository of the project is here [https://github.com/opencb/iva](https://github.com/opencb/iva).
+
+Default _**develop**_ branch can be downloaded by executing:
+
+```text
+$ git clone https://github.com/opencb/iva.git
+Cloning into 'iva'...
+remote: Enumerating objects: 126, done.
+remote: Counting objects: 100% (126/126), done.
+remote: Compressing objects: 100% (72/72), done.
+remote: Total 10370 (delta 70), reused 85 (delta 38), pack-reused 10244
+Receiving objects: 100% (10370/10370), 4.70 MiB | 61.00 KiB/s, done.
+Resolving deltas: 100% (6064/6064), done.
+```
+
+Latest stable release at _**master**_ branch can be downloaded by executing:
+
+```text
+$ git clone -b master https://github.com/opencb/iva.git
+Cloning into 'iva'...
+remote: Counting objects: 624, done.
+remote: Total 624 (delta 0), reused 0 (delta 0), pack-reused 624
+Receiving objects: 100% (624/624), 139.37 KiB | 191.00 KiB/s, done.
+Resolving deltas: 100% (356/356), done.
+Checking connectivity... done.
+```
+
+After this, in both cases, you **must** execute the following command to fetch the JSorolla submodule \(only the first time\):
+
+```text
+git submodule update --init
+```
+
+Go to `./lib/jsorolla` and checkout to _**develop**_ branch of Jsorolla by
+
+```text
+cd lib/jsorolla
+git checkout develop
+npm run install
+```
+
+### Run
+
+To run IVA in dev mode \(hot reload for CSS files and hot restart, aka "live reloading", for JS scripts\), run
+
+`npm run serve`.
+
+### Build
+
+To produce the built version, just run
+
+`npm run build`.
+
+### Test
+
+We use [Cypress.io](https://www.cypress.io/) as testing framework.
+
+Having the project running through the command `npm run serve`, you can run the **interactive E2E** test suite by running the command
+
+```text
+npm run e2e
+```
+
+or the **headless E2E** test suite \(no browser window\).  
+This mode comes with an HTML report \(generated in `./report`\).
+
+```text
+npm run e2e-report
+```
+
+in a Windows environment, just add the suffix `-win`
+
+```text
+npm run e2e-win
+npm run e2e-report-win
+```
+
diff --git a/docs/overview.md b/docs/overview.md
@@ -0,0 +1,26 @@
+# Overview
+
+Interactive Variant Analysis \(IVA\) is a web application for filtering, analysis and interpretation of population-scale genotype data. This interactive tool allows the identification of genes affected by deleterious variants that segregate along family pedigrees, case-control or sporadic samples.
+
+IVA has been developed as part of the [OpenCGA](http://docs.opencb.org/display/opencga/Welcome+to+OpenCGA) project, making it easy to work with clinical and variant information stored in a Catalog and Variant storage instance.
+
+## Main Features
+
+* **Authenticated** and **secure** platform to query and visualise data
+* Fully **customizable platform** and extensible though **pluggings**
+* Multiple tools and analysis available:
+  * Advanced **variant filtering**: filter your variants 
+  * **Genome browser**
+  * **Clinical analysis**
+  * **Aggregation analysis**
+* Allow to load VCF files and samples together with clinical data
+* High-performance and scalable VCF and gVCF indexing
+* VCF normalization and variant annotation
+* Clinical interpretation analysis of samples and families
+
+### Contact
+
+* Ignacio Medina 
+
+ ⚠ IVA is developed and maintained by the [University of Cambridge](https://www.cam.ac.uk/) and [Genomics England](https://www.genomicsengland.co.uk/). It is freely available at [**https://github.com/opencb/iv**](https://github.com/opencb/iva)
+
diff --git a/docs/user-manuals/case-interpreter.md b/docs/user-manuals/case-interpreter.md
@@ -0,0 +1,6 @@
+# Case Interpreter
+
+The Case Interpretation is the most relevant of the IVA’s components for a Clinical Scientist. The cases created and its associated data can be found in the Case Portal within the Case Interpretation tab. You can access the space from the top-tab or from the central display of the screen _\( as highlighted in the picture with red arrows\)._
+
+![](../.gitbook/assets/image%20%287%29.png)
+
diff --git a/docs/user-manuals/catalog-browser.md b/docs/user-manuals/catalog-browser.md
@@ -0,0 +1,2 @@
+# Catalog Browser
+
diff --git a/docs/user-manuals/iva-general-usage.md b/docs/user-manuals/iva-general-usage.md
@@ -0,0 +1,33 @@
+# IVA General Usage
+
+{% hint style="info" %}
+_**NOTE**_: _You can access our public IVA installation at the University of Cambridge at_ [_http://bioinfo.hpc.cam.ac.uk/web-apps/iva-prod/\#home_](http://bioinfo.hpc.cam.ac.uk/web-apps/iva-prod/#home)_._ The current version of IVA for the installation is_**`V2.0.0-RD`**_
+{% endhint %}
+
+## Login
+
+Navigate to the IVA main page. For example, if you want to access the University installation, go this [link](http://bioinfo.hpc.cam.ac.uk/web-apps/iva-prod/#home) , find the **Login tab** in the top right of the screen and introduce the credentials: user: _demouser_, password: _demouser._
+
+![IVA&apos;s Login page](../.gitbook/assets/image%20%282%29.png)
+
+If the credentials provided are correct, a "Welcome Message" will be displayed and the application will start to fetch the studies populated into the correspondent OpenCGA installation you are accessing to.
+
+![](../.gitbook/assets/image%20%285%29.png)
+
+##  Project and Studies
+
+### **Project and Study organisation**
+
+The project/study organisation is  key in order to optimise data usability in OpenCGA, and thus in IVA.
+
+Projects provide physical separation of data into different database tables.  
+Studies provide logical separation of data within a Project. For an efficient project/study organisation, see next recommendations: 
+
+* Data from different genome assemblies should keep in different projects \(e.g you should create a project for data from GRCh37 and other for data from GRCh38\)
+* It is appropriate to store  data in different projects when there is no foreseeable need to process them jointly.
+* It is recommended to split your data in studies corresponding to different independent datasets that may be used together in some analysis, with the aim of having homogeneous datasets for each study.
+
+![](../.gitbook/assets/image%20%286%29.png)
+
+## Explore the different components of IVA
+
diff --git a/docs/user-manuals/variant-analysis.md b/docs/user-manuals/variant-analysis.md
@@ -0,0 +1,2 @@
+# Variant Analysis
+
diff --git a/docs/user-manuals/variant-browser.md b/docs/user-manuals/variant-browser.md
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+# Variant Browser
+
+## Overview
+
+The Variant browser allows you to view and filter variants for your chosen study using multiple parameters, which can be found in the left-hand menu. The filters available are: 
+
+### Filters  <a id="IVAuserguide-Applyingfilters"></a>
+
+### Applying filters <a id="IVAuserguide-Applyingfilters"></a>
+
+* **Studies**
+  * For studies on the within the same project \(RD38 & CG8\) you can apply AND/OR logic to filter for variants present in both studies or either one of the studies. Select the logic and tick the appropriate box fir your study of choice
+* **Genomic**
+  * Chromosomal location \(by genomic coordinate\)
+  * Feature IDs \(genes, SNPs, transcripts\)
+  * Gene disease panels \(genes included in the chosen [PanelApp ](https://panelapp.genomicsengland.co.uk/)panels\)
+  * Biotype \(gene or transcript type\)
+  * Variant type - SNV \(single nucleotide variant\), MNV \(multiple nucleotide variant\), CNV \(copy number variant\), SV \(structural variant\) or INDEL \(insertion/deletion\)
+* **Population frequency**
+  * Population frequency as calculated overall or by population group in the 1000 Genomes and gnomAD databases
+* **Consequence type**
+  * Consequence type SO \(Sequence ontology\) terms. You can filter for all Loss-of-Function terms here
+* **Deleteriousness**
+  * Deleteriousness of variant using prediction tools SIFT, Polyphen and CADD \(NB that CADD is only available in GRCh37 studies\)
+* **Conservation**
+  * Conservation score as calculated by PhyloP, PhastCons and Gerp.
+* **Gene ontology**
+  * Gene ontology terms describing gene function
+* **Phenotype-disease**
+  * HPO \(human phenotype ontology\) accession IDs
+  * ClinVar accession IDs
+  * Full-text search on HPO, ClinVar, protein domains or keywords, and some OMIM and Orphanet IDs
+
+Once you have defined your filters, click **Search** to show the resulting variants in table format, as in the screenshot below. \(Summary format is not yet available.\)
+