Variant prioritisation Flashcards
1
Q
What are the 2 methods of filtering a VCF file?
A
- annotation based- Intronic variants, 5’ UTR and variants above a certain AF e.g. 1%
- Quality based- Using QUAL scores (Alignment score) or depth criteria (DP)
2
Q
What are the 4 steps in variant prioritisation?
A
- Filtering variants <1% in population frequency databases (gnomAD and 100 genomes project)
- Prioritise based on functionality-
High priority- Stop loss/gain, non-synonymous AA changes
Low priority- Synonymous AA changes - Prioritise variants that have been previously associated with the disease phenotype of the referred patient (OMIM)
- Selection of variants in combination with other information such as Pubmed and in-silico tool analysis