Briefly describe the feature and provide meaningful references
Transcript annotation for variants needs to be changed to match AutoPVS1 annotation, rather than using PICK, since we are correcting PVS1 based on this transcript.
What input data are required for this feature or analysis?
All input files for AutoGVP (vep-annotated vcf, multianno, intervar, autopvs1 files)
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
modify 01-annotate_variants_CAVATICA_input.R and 01-annotate_variants_custom_input.R to retain autopvs1 transcript annotation.
modify 04-filter_gene_annotations.R to retain VEP results only for transcripts selected by autopvs1 workflow for each variant.
Who will complete the feature request (please add a GitHub handle here if relevant)?
Purpose/implementation Section
Briefly describe the feature and provide meaningful references
Transcript annotation for variants needs to be changed to match AutoPVS1 annotation, rather than using PICK, since we are correcting PVS1 based on this transcript.
What input data are required for this feature or analysis?
All input files for AutoGVP (vep-annotated vcf, multianno, intervar, autopvs1 files)
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
01-annotate_variants_CAVATICA_input.Rand01-annotate_variants_custom_input.Rto retain autopvs1 transcript annotation.04-filter_gene_annotations.Rto retain VEP results only for transcripts selected by autopvs1 workflow for each variant.Who will complete the feature request (please add a GitHub handle here if relevant)?
@rjcorb