What feature is being added or bug is being addressed?
Closes #211. This PR updates AutoGVP cavatica workflow to allow for input of and annotation with an external clinvar vcf, to replace any clinvar annotation in sample VCFs.
What was your approach?
Updated run_autogvp.sh to allow for clinvar vcf argument when running 02-annotate_variants_CAVATICA_input.R.
Updated 02-annotate_variants_CAVATICA_input.R to include conditional statements dependent on whether ClinVar calls should be made with sample VCF annotations vs external ClinVar vcf.
What GitHub issue does your pull request address?
211
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. @jungkim2, can you determine if RMS calls are the same between cavatica and custom workflow when using the Oct 2023 clinvar vcf as input?
Is there anything that you want to discuss further?
I have run the RMS dataset through the updated cavatica workflow WITHOUT external clinvar vcf, and results match those from the previous AutoGVP version. I have also run the dataset through the updated workflow WITH the Oct 2023 clinvar vcf as input, and there are ~1000 different calls that seem to be due to new ClinVar submissions since May 2022 (ClinVar version used by cavatica workflow by default).
Purpose/implementation Section
What feature is being added or bug is being addressed?
Closes #211. This PR updates AutoGVP cavatica workflow to allow for input of and annotation with an external clinvar vcf, to replace any clinvar annotation in sample VCFs.
What was your approach?
run_autogvp.shto allow for clinvar vcf argument when running02-annotate_variants_CAVATICA_input.R.02-annotate_variants_CAVATICA_input.Rto include conditional statements dependent on whether ClinVar calls should be made with sample VCF annotations vs external ClinVar vcf.What GitHub issue does your pull request address?
211
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. @jungkim2, can you determine if RMS calls are the same between cavatica and custom workflow when using the Oct 2023 clinvar vcf as input?
Is there anything that you want to discuss further?
I have run the RMS dataset through the updated cavatica workflow WITHOUT external clinvar vcf, and results match those from the previous AutoGVP version. I have also run the dataset through the updated workflow WITH the Oct 2023 clinvar vcf as input, and there are ~1000 different calls that seem to be due to new ClinVar submissions since May 2022 (ClinVar version used by cavatica workflow by default).