Briefly describe the feature and provide meaningful references
ClinVar's variant_summary.txt and submission_summary.txt files are currently loaded in AutoGVP scripts to select submissions used for resolving conflicting pathogenicity calls. However, running this with every sample is redundant as well and time- and memory-intensive, so it should be moved to a separate script to be run prior to running AutoGVP.
What input data are required for this feature or analysis?
submission_summary.txt and variant_summary.txt files.
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
Relevant code will be transferred from 01-annotate_variants_CAVATICA_input.R/01-annotate_variants_custom_input.R to new R script.
Who will complete the feature request (please add a GitHub handle here if relevant)?
rjcorb
commented
1 year ago
Purpose/implementation Section
Briefly describe the feature and provide meaningful references
ClinVar's
variant_summary.txtandsubmission_summary.txtfiles are currently loaded in AutoGVP scripts to select submissions used for resolving conflicting pathogenicity calls. However, running this with every sample is redundant as well and time- and memory-intensive, so it should be moved to a separate script to be run prior to running AutoGVP.What input data are required for this feature or analysis?
submission_summary.txtandvariant_summary.txtfiles.How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
Relevant code will be transferred from
01-annotate_variants_CAVATICA_input.R/01-annotate_variants_custom_input.Rto new R script.Who will complete the feature request (please add a GitHub handle here if relevant)?
@rjcorb