Briefly describe the feature and provide meaningful references
CSQ field names need to be extracted from VEP-annotate vcf files to be used as column names in AutoGVP final output.
What input data are required for this feature or analysis?
VEP-annotated VCF file
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
bcftools vep-plugin can be run in parse_vcf.sh script to create a tsv file of field names. This can then be used as input in 04-filter_gene_annotations.R script.
Who will complete the feature request (please add a GitHub handle here if relevant)?
naqvia
commented
1 year ago
Purpose/implementation Section
Briefly describe the feature and provide meaningful references
CSQfield names need to be extracted from VEP-annotate vcf files to be used as column names in AutoGVP final output.What input data are required for this feature or analysis?
VEP-annotated VCF file
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
bcftools vep-plugin can be run in
parse_vcf.shscript to create a tsv file of field names. This can then be used as input in04-filter_gene_annotations.Rscript.Who will complete the feature request (please add a GitHub handle here if relevant)?
@rjcorb