broadinstitute/seqr

web-based analysis tool for rare disease genomics

seqr's Issues

"Go back" click on modals

Sometimes takes a couple clicks - something wrong with event propagation

Order projects by most recent access

We need a way to get all the projects in xbrowse in order of the most recent access - so we can reload projects in a logical order.

Gene search across project

This is top application-level priority right now! Working on a hack in branch project_gene_search.

Consistent naming for "quality filter" and "genotype quality filter"

why isn't JS minified?

Family variants page

Sahar points out it's broken

Gene list inputs with non-ascii characters

Generates a server error

Move add_extra_* calls out of views.py

This is horrible design

Command line interface for annotator

This will allow us to load a full annotator for all projects without taking xbrowse offline

Show variant notes for whole project in search results

Right now variant notes only show up in search results if a note was added for the particular family being searched. That's bad! We should show a note for family A in the search results for family B.

Show AC and AN along with AF

Clearly we need this for all the ExAC populations, but I'm not sure the best way to do it. Maybe we show when you hover over the allele frequncies in the variant list?

Include CNVs in Mendelian search

Ideally both XHMM and ExomeDepth CNVs could be included as variants in exome-wide Mendelian search. xBrowse currently only supports ExomeDepth CNVs and only in Diagnostic Search mode; we have no other tool for finding causal CNVs in our patients.

Integrate minimal_representation

Add LOFTEE to xbrowse annotations

Support for smarter denovo calls

We need to support Kaitlin's Samocha's de novo methods, or something like it. Not sure if we should support trio-aware variant calls. More to come...

All Cohort searches don't work

Make annotator aware of which VCF files it's seen

datastore does not accept None as filters

500 error for variant list if project not loaded

Should have better error handling here

Ref and alt alleles aren't minrep'd

Minrep integration is finished, but the ref and alt alleles are still displayed with their pre-minrep versions. Annoying!

When listing causal variants, currently only the genomic position and changed is displayed.

At the very least, can we also have the gene itself.

Filter out ICE-specific intervals

Double top priority

gene autocomplete should not stop at 10 results

Export saved variants

Screen re-direction after flagging/submitting causal variant

This is annoying and assumes there is only one causal variant when there may be two in one gene

Single family / variant view

Should be able to link to a single variant in a family, instead of saying "the third variant in this search result".

Remove custom_annotator nonsense

We want the annotator to be flexible, but we did it in the wrong way. Should merge everything into a single Annotator class, and just have optional fields. Assigning to me because I can clean up the mess pretty quickly.

Rewrite edit-individuals page

This page has gotten worse over time. Plan is to:

• move pedigree editing to edit-family page
• create a new edit-families page just for setting which individuals are in which families
• treat phenotypes totally separately

pooled variant list that is ordered by family

In a project, just show all the variants ordered by family

Better causal variants page

Should show a list of families with inheritance mode and causal variants, not just a simple list

In variant download, DP and GQ are switched

Project listing page - redesign/reformatting

The aesthetics of this page compared to the others is a big outlier. It's not an urgent thing but something to think about.

Gene notes and tags

Should discuss this

Ensembl database connections should be lazy loaded

So xbrowse works offline

Include HGVS in VEP output

Add # of families to family group page

And cohort page if necessary

Rename VariantFilter to AnnotationFilter globally

Start using global variant namedtuple

Family variants page

There is no link on the family page or a summary regarding variants flagged for that family. The only way currently to get this is through the projects page which is a dump of all flagged variants for that project without the ability to sort.

After flagging a variant, the flag does not immediately appear in the current results page

Remove or flag annotations to clearly out of frame transcripts

Minirep all variant input in xBrowse

I remember sitting down with Eric discussing minirep last year...then we never actually added it to xBrowse! This is super important and I think it's a good time to do it now.

The challenge will be making sure we are comprehensive, as there are a bunch of different variant input sources. I'm going to use this ticket to make a list of all the inputs we need to check.

Candidate novel gene search across cohorts

These request are becoming more often amongst our collaborators.

Custom population frequency filters are broken

Create comprehensive data check

Single script that checks for things like:

• data in resources that isn't part of the family set
• any IDs with spaces or punctuation in them
• ...will add more

Write so this can be pulled into continuous integration at some point

Delete saved variants

Causal variants aren't highlgithed in MVS

Saved variants project page - no link back to family

Support for chrMT

Will require some refactoring of genomeloc.py

Sorting on the families page