update select-clinvar-submissions.R to only consider P,LP,B,LB,VUS submissions

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #222. This PR updates select-clinvar-submissions.R to retain only P,LP,B,LB, and VUS submissions when attempting to resolve ClinVar variants with conflicting interpretation.

What was your approach?

Removed all submissions for which ClinicalSignificance did not equal one of the above values.

What GitHub issue does your pull request address?

222.

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please re-run select-clinvar-submissions.R and ensure that ClinicalSignificance is only equal to P,LP,B,LB, or US in output.

Rscript scripts/select-clinVar-submissions.R --variant_summary data/variant_summary.txt.gz --submission_summary data/submission_summary.txt.gz --outdir results --conceptID_list data/clinvar_all_disease_concept_ids.txt --conflict_res "latest"

Is there anything that you want to discuss further?

I will submit a separate PR to make sure that variants with "unconventional" ClinVar clinical significance (see [Variant ID 822](https://www.ncbi.nlm.nih.gov/clinvar/variation/822/?oq=822&m=NM_000038.6(APC):c.3920T%3EA%20(p.Ile1307Lys) as an example) are resolved by ClinVar during AutoGVP run.

Documentation Checklist

• [X] The function has examples to showcase the usage

[rjcorb]

@rebkau I think this will resolve the issue with the APC variant. Can you run AutoGVP on that sample and see if the correct call is made (LP, ClinVar)?

[naqvia]

Works for me as well!