✏️ update docs with bench critieria #20
Conversation
| - PASS+GNO 0.003%: Applied the HIVE gnomAD filter (exclude gnomad >= 0.00003) directly to the PASS file. I used this as a comparison to see just how much value we were getting from the other filtration steps | ||
| - PASS+PON: Removed any records from the PASS file that were also found in the GATK PON | ||
| - PASS+PON+dbSNP: Removed any records from PASS+PON that were labeled COMMON in dbSNP | ||
| - PASS+PON+dbSNP+ClinVar: Removed any records from PASS+PON+dbSNP that had "benign" in their worst VEP assigned CLN_SIG |
There was a problem hiding this comment.
This seems unclear to me what it means reading as someone who has not used this pipeline before:
"had "benign" in their worst VEP assigned CLN_SIG"
There was a problem hiding this comment.
It's VEP jargon. CLN_SIG is the VEP key for "ClinVar clinical significance of the dbSNP variant". See Default VEP output. ClinVar significance is just an annotation about the significance of any given variant: https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/#clinsig_scv.
VEP can assign many different consequences to the variants based on the alternative alleles. The concept of "worst" comes into play when you have a lot of different annotations for a given variant. In that case, you often want to check what's the "worst" case scenario for that variant.
So what this sentence is saying is: for any given variant, look through all the annotations and see what the worst ClinVar significance is. If its "only" benign, then we drop the variant.
| - PASS+GNO 0.003%: Applied the HIVE gnomAD filter (exclude gnomad >= 0.00003) directly to the PASS file. I used this as a comparison to see just how much value we were getting from the other filtration steps | ||
| - PASS+PON: Removed any records from the PASS file that were also found in the GATK PON | ||
| - PASS+PON+dbSNP: Removed any records from PASS+PON that were labeled COMMON in dbSNP | ||
| - PASS+PON+dbSNP+ClinVar: Removed any records from PASS+PON+dbSNP that had "benign" in their worst VEP assigned CLN_SIG |
There was a problem hiding this comment.
It's VEP jargon. CLN_SIG is the VEP key for "ClinVar clinical significance of the dbSNP variant". See Default VEP output. ClinVar significance is just an annotation about the significance of any given variant: https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/#clinsig_scv.
VEP can assign many different consequences to the variants based on the alternative alleles. The concept of "worst" comes into play when you have a lot of different annotations for a given variant. In that case, you often want to check what's the "worst" case scenario for that variant.
So what this sentence is saying is: for any given variant, look through all the annotations and see what the worst ClinVar significance is. If its "only" benign, then we drop the variant.
Description
This adds our benchmarking story behind our filtering criteria for tumor-only calling
Fixes # https://d3b.atlassian.net/browse/BIXU-1928
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: