Rjcorb/173 add descriptive clinvar revstat

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #173. This PR creates a descriptive clinvar review status column that indicates how a call was made in cases where variants have conflicting interpretations, and includes both this and original review status columns in final output.

What was your approach?

• Modified select-clinVar-submissions.R script to include additional descriptors in ReviewStatus column when variants had conflicting interpretations: criteria provided, conflicting interpretations, consensus call taken or criteria provided, conflicting interpretations, latest date evaluated call taken.
• Modified annotate_variants_*_input.R scripts to include updated ReviewStatus column in intermediate output.
• Modified output_colnames.tsv to include updated ReviewStatus column, and remove redundant ClinVar annotation columns from output.

What GitHub issue does your pull request address?

173

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

Which areas should receive a particularly close look?

Please first run select-clinVar-submissions.R and confirm that variants with conflicting interpretations have additional descriptor:

`select-clinVar-submissions.R --variant_summary input/variant_summary.txt.gz --submission_summary submission_summary.txt.gz

Then run AutoGVP to confirm that column clinvar_review_status_autogvp is included in final output:

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

Is there anything that you want to discuss further?

Documentation Checklist

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