Entering edit mode
4.2 years ago
Martina
▴
30
Dear colleagues,
If you wanted to be sure that VCF from exome tumour-normal sequencing, focused on somatic variants you got from someone was done properly and you would believe BAM preparation and data quality, what would you check?
I would go for:
- in baits filter
- QUAL filter
- indels in homopolymer
- amount of reads supporting alt variant
- % of reads supporting alt variant
- 0 alt reads in normal tissue control
- min coverage
- max coverage (2x median)
- low complexity regions
Filtering by databases: - ExAC - SIFT - PolyPhen
What would you add? I can't find a list of existing filters anywhere. Do you have some favourite paper where they have done really precise filtering?
Thank you very much, Martina
