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Glue between Clinical Genomics apps
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Allow scout loading of STR VCFs #201

Closed dnil closed 5 years ago

dnil commented 6 years ago

Short tandem nucleotide repeats can expand to cause genetic disease. ExpansionHunter can detect targeted STRs from bam files and generate VCFs. Scout can display these.

Problem: MIP generates STR VCFs with ExpansionHunter: #252 Recorded in qc_sampleinfo.yaml:

[FAMILY_ID]:
  expansionhunter:
    Path: [path/file.vcf]

Sample info key for ExpansionHunter VCF to enter scout case load config: #787 #968 

family: '643594'
...
vcf_str: scout/demo/643594.clinical.str.vcf.gz

Suggested solution:

To do:

Q: How to view in Scout? A: Ask DN, MM and CR, action EOL

DoD:

emiliaol commented 6 years ago

mip 7

henrikstranneheim commented 6 years ago

yes

barrystokman commented 5 years ago

@henrikstranneheim @jemten

Trailblazer is parsing _qc_sample_info.yaml, and is expecting a key program in that file. The MIP7.1 sample info file I'm using (justhusky) does not have that key. Before I start changing things in TB, is that intentional?

Example: TB is trying to get the path below (example from MIP6) but throws a KeyError for key program for MIP7.1

program:
  ...
  svdb:
    path: /home/proj/stage/rare-disease/cases/grownliger/analysis/grownliger/bwa/grownliger_sorted_md_brecal_comb_SV.vcf

edit: TB also expects something (data['program']['genmod']['rank_model']['version']) for rank_model_version

henrikstranneheim commented 5 years ago

Yes, it is intentional. We have replaced “program” with “recipe” as it is a better description of the actual code.

I know this yaml is a bit complex, but it is hard to represent all this information in a simple manner. You can perhaps be a little wiser by looking at the description of the file here: https://github.com/Clinical-Genomics/MIP/blob/master/documentation/API/Sample_info.md. It would be great to sit together for this one to explain. However, I guess mail will have to do for now. Please, Let me know if you have more questions.

barrystokman commented 5 years ago

Last task: fix unit tests