What feature is being added or bug is being addressed?
Closes #169. This PR updates selection of ClinVar submissions based on consensus call by merging L/LP and B/LB variants together when counting submissions, rather than considering these classifications separately as was done previously.
What was your approach?
Modified code in select-clinVar-submissions.R to create a new column ClinSig that takes values P/LP, B/LB and VUS. Submissions for each VariationID were counted based on ClinSig column to identify variants with a majority call. Then, among calls in this majority group, the classification at the most recently evaluated date is taken as final call.
What GitHub issue does your pull request address?
169
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please review updated code and run select-clinVar-submissions.R:
Purpose/implementation Section
What feature is being added or bug is being addressed?
Closes #169. This PR updates selection of ClinVar submissions based on consensus call by merging L/LP and B/LB variants together when counting submissions, rather than considering these classifications separately as was done previously.
What was your approach?
Modified code in
select-clinVar-submissions.Rto create a new columnClinSigthat takes valuesP/LP,B/LBandVUS. Submissions for eachVariationIDwere counted based onClinSigcolumn to identify variants with a majority call. Then, among calls in this majority group, the classification at the most recently evaluated date is taken as final call.What GitHub issue does your pull request address?
169
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Please review updated code and run
select-clinVar-submissions.R:Rscript select-clinVar-submissions.R --variant_summary input/variant_summary.txt.gz --submission_summary input/submission_summary.txt.gzIs there anything that you want to discuss further?
No
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