Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #148. This PR modifies code in 01-annotate_variants_*_input.R so that ClinVar calls with conflicting interpretation that are resolved with submissions have Stars == 1 in final output.

What was your approach?

All calls with initial Stars == "1NR were set to "1" in master_tab output

What GitHub issue does your pull request address?

148

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

Which areas should receive a particularly close look?

Please run autogvp bash script on test pbta and custom files, and ensure that all calls with ClinVar have a value in clinvar_stars.

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 INFO/DP>=15 (gnomad_3_1_1_AF_non_cancer<0.01|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=input/test_pbta.hg38_multianno.txt.intervar \
--multianno=input/test_pbta.hg38_multianno.txt \
--autopvs1=input/test_pbta.autopvs1.tsv \
--outdir=../results \
--out="test_pbta"

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

diskin-lab-chop / AutoGVP

Set resolved ClinVar calls to Stars == "1" #149