Current README file lacks some information as developers, license, ...

• Implement a text box by means of which HPO terms can be selected
• Implement a list of the selected HPO terms from which terms can be removed
• Implement a graphical view of the HPO hierarchy to select the level to select entire branches of the HPO hierarchy
• The selected terms can be used to filter in or to filter out

Use the Gencode basic annotation already included in CellBase.
Modify queries to get only basic transcripts

Use the Gencode basic annotation already included in CellBase.
Include flab basic in OpenCGA

• Implement a text box by means of which GO terms can be selected
• Implement a list of the selected GO terms from which terms can be removed
• Implement a graphical view of the GO hierarchy to select the level to select entire branches of the GO hierarchy
• The selected terms can be used to filter in or to filter out

Add all consequence types and transcripts to the grid.

All OpenCB projects are migrating to Apache License 2.0. This could be also applied to BierApp.

This documentation needs to cover the main Biearpp options:

• Loading samples
• View selected samples in Variant Browser
• Search variants with differents filters
• Variant data

I can upload a VCF file but it is not possible to index this one. So we can't work with BiERapp.
Please, a clue to solve it!

Some tweaks need to be done in the web:

• First fitler section shold be called 'Sample filter'
• Analysis/Study type must be moved to 'Sample filter'
• The study object passed to the grid component must include the name for adding a title

Select samples are not shown in the Segregation filter.

It says:

bower network-viewer#develop             ECMDERR Failed to execute "git ls-remote --tags --heads [email protected]:bioinfo/network-viewer.git", exit code of #128 ssh: Could not resolve hostname gitlab.bioinfo.cipf.es: No address associated with hostname fatal: Could not read from remote repository.  Please make sure you have the correct access rights and the repository exists.

This is a typical cancer filter. Consists on subtracting from obe VCF (somatic) the variants already found in other VCF (germinal). Missing values in the germinal must be taken into account.

Add the case/control filter in the interface

Only the first gene is shown now in the grid table, all of them should be shown.

Implement the additionalAttribute index in OpenCGA (in coordination with cambridge)

• Check input formats GFF, BED
• Check annotation
• Check indexes
• Ckack quieries on the indexes

Implement the following indexes already available in CellBase (check with Javier Lopez if needed):

• HPO
• GO
• CADD
• Tissue gene expression

Currently both 1000G Phase 1 and 3 frequencies are shown in the main variant grid. Having 1000 G Phase 3 makes unnecessary the Phase 1, theses should be removed.