logust79

Demo evaluation needs correction

5

In the demo's Evaluation section, the command: ``` zcat /tmp/gHapMixDemo/TempCNV_child1/CNV.vcf.gz | grep -v ":REF:" > /tmp/gHapMixDemo/TempCNV_child1/CNV.vcf (remove REF calls) /CanvasDIR/Tools/EvaluateCNV/EvaluateCNV.dll /ihart/BaseSpace/Projects/CanvasSPW/AppResults/simdata/Files/child1_truth.bed /tmp/gHapMixDemo/TempCNV_child1/CNV.vcf /CanvasDIR/Tools/EvaluateCNV/generic.cnaqc.excluded_regions.bed inheritedCNVs.txt ``` would not run since the...

First thanks for this work. Works very well. Whilst I'm testing it, it issues a warning: ``` WARNING:tensorflow:: Using a concatenated state is slower and will soon be deprecated. Use...

`sex` and `solved` fields missing from `mongodb.test_patients.patients`

2

would be best to add those fields in as some future analyses might rely on these

File "/home/rmhanpo/phenopolis/templates/variant.html", line 55, in block "body" {% if variant.AF %}{{ '%0.4g' % variant.AF }}{% else %}NA (Allele Number = 0){% endif %} TypeError: float argument required, not unicode

got a `key_error` when trying to see patients that I don't have access to.

2

KeyError KeyError: 'external_ids' ```python File "/home/rmhanpo/phenopolis/views/individual.py", line 73, in individual_page if not lookup_patient(db=get_db(app.config['DB_NAME_USERS']),user=session['user'],external_id=individual): return 'Sorry you are not permitted to see this patient, please get in touch with us to...

request auth mean json route not easily queriable from command line

2

such as https://uclex.cs.ucl.ac.uk/hpo_json/HP:0000556 @requires_auth doesn't seem to accept requests' auth arguments. If we use the single-login method mentioned in #3 this will make the API much more useful.

Visualisation of causal variants location on protein domains.

1

Possibly something like this: https://decipher.sanger.ac.uk/gene/EP300#overview/protein-info Or like this: http://www.rcsb.org/pdb/protein/P78509

mark variant as not real

1

some variants, when verified with Sanger sequencing, are not real. How do we effectively integrate this info into the database?

This is primarily for individual diagnosis. When new evidence comes in, say a new release triggering new variant call, or cnv data get merged in, the following may happen: -...