This is the plan for implementing transcript filtering:
Requirements:
independent of VEP module. VEP output annotates as default all transcripts, which should be an intermediate output for QC and resuming the workflow with different transcript filtering without rerunning VEP annotation.
should accept VEP-annotated VCFs as input.
Features:
Filtering based on provided list of transcripts.
Filtering for only ONE transcript per variants based on PICK flag.
The PICK flag has an ordered set of criteria for choosing the PICK transcript, including MANE, CANONICAL, APPRIS, consequence, etc.. Can be adapted using a separate parameter --pick_order. More information here.
Filtering based on specific annotation, which also allows multiple transcripts per variant including: MANE_PLUS_CLINICAL, MANE_SELECT, CANONICAL
Should not drop variants , but annotations if variants do not match any transcript (no silent dropping of variants!).
Description of feature
This is the plan for implementing transcript filtering: Requirements:
Features: