puzzle

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This would create a way to narrow the analysis to custom regions

moonso

Add annotations

4

Creating this issue to gather similar issues in one. In general we need suggestions of how to pick these from the vcf, what are the common named keys, are they...

moonso

henrikstranneheim

Show some feedback when loading variants

1

It takes a couple of seconds to load 10K variants in memory, would be nice to give some feedback to the user. Something like for example a modal saying that...

guillermo-carrasco

This is a project that we could use but it only works on OSX https://github.com/burrows-labs/pyship

robinandeer

Indicate which variants have comments in the variants listing page

1

...and allow listing/filtering of only "tagged"/commented variants

vasiliosz

Access gemini's --gt-filter for custom queries in gemini adapter?

5

I use these all the time when working directly against gemini. http://gemini.readthedocs.org/en/latest/content/querying.html#gt-filter-filtering-on-genotypes For example: ``` gemini query --header \ -q "SELECT chrom,start,end,gene,impact,impact_severity,codon_change,aa_change,aa_length, \ cadd_scaled,clinvar_gene_phenotype,(gts).(*),(gt_ref_depths).(*),(gt_alt_depths).(*) \ FROM variants WHERE (max_aaf_all

vasiliosz

External links

2

Would be nice to have (hardcoded for now): - [ ] HPA - [ ] entrez - [ ] STRING - [ ] Reactome

henrikstranneheim

Improve filtering ui

7

Here are some suggestions for improving the filtering ui: - [ ] Sliders as input for numeric inputs: frequency filtering, CADD scores and (not implemented) SV size for example -...

vasiliosz

henrikstranneheim