Flag conflicting clinvar variants with >= 1 P/LP submission in final output

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #191. This PR creates a column clinvar_flag that makes note of conflicting ClinVar variants with at least 1 P/LP submission to be saved to final output. This will allow users to manually review such calls to and resolve them in a manner that aligns with study goals.

What was your approach?

• added clinvar_flag column to output of select-clinVar-submissions.R and saved to output. This column has values "Variant has conflicting interpretations in ClinVar and at least 1 submission with P/LP call" or "None" for ClinVar variants, and NA for variants not found in ClinVar.
• Appended clinvar_flag column to output of 02-annotate_variants_*_input.R
• Added clinvar_flag to output_colnames.tsv so that it is saved to final AutoGVP output.

What GitHub issue does your pull request address?

191

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

Which areas should receive a particularly close look?

Please check updated code logic, and rerun select-clinVar-submissions.R from root to generate new ClinVar-selected-submissions.tsv file with clinvar_flag column:

Rscript scripts/select-clinVar-submissions.R --variant_summary data/variant_summary.txt.gz --submission_summary data/submission_summary.txt.gz --outdir results

Then run custom workflow on test custom files from root, to ensure that conflicting variants are reported as expected (there are no such conflicting variants with p/lp submissions in pbta test files):

bash run_autogvp.sh --workflow="custom" \
--vcf=data/test_VEP.vcf \
--clinvar=data/clinvar.vcf.gz \
--intervar=data/test_VEP.hg38_multianno.txt.intervar \
--multianno=data/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=data/test_autopvs1.txt \
--outdir=results \
--out="test_custom"

Is there anything that you want to discuss further?

No

Documentation Checklist

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