It would be convenient to produce an additional variants.annotated.tsv from the final VCF that is produced for pvacseq.
This could be much the same as the table that already produced but add RNA counts by adding these fields to the genotype_fields: RAF and RAD
The report would be generated in a two step process involving: GATK VariantsToTable and VAtools (vep-annotation-reporter).
This new step could mirror and/or reused the existing YAML inputs to decide which information to put in the report but have the report generated later in the pipeline instead of inside detect-variants:
If the GATK variants to table tools works even if one of these is missing, then the same exact lists could be reused on the detect variants VCF and the final pVACtools VCF.
It would be convenient to produce an additional variants.annotated.tsv from the final VCF that is produced for pvacseq.
This could be much the same as the table that already produced but add RNA counts by adding these fields to the genotype_fields:
RAFandRADThe report would be generated in a two step process involving: GATK VariantsToTable and VAtools (vep-annotation-reporter).
This new step could mirror and/or reused the existing YAML inputs to decide which information to put in the report but have the report generated later in the pipeline instead of inside detect-variants:
immuno.vep_to_table_fields immuno.variants_to_table_fields immuno.variants_to_table_genotype_fields
If the GATK variants to table tools works even if one of these is missing, then the same exact lists could be reused on the detect variants VCF and the final pVACtools VCF.