Extract-de-novo-mutations-from-trio

Project completed during my MSc in Bioinformatics at the University of Birmingham, United Kingdom, 2019-2020.

Data pre-processing

1. QC & FILTERING
   • pass threshold lod≥3
   • exclude missing variants
   • exclude multi-allelic variants
   • exclude low no of reads - only keep ≥30
   • exclude low PHRED scores - only keep≥20

Data analysis

• uses vcfR R package

1. EXTRACT GENOTYPE (reference allele vs. alternative allele e.g. 0/1)
2. EXTRACT DNA BASES (reference allele vs. alternative allele)
3. FIND THE CHILD (count the no of incompatible variants)
4. EXTRACT DE NOVO VARIANTS FROM THE CHILD
5. FURTHER RESEARCH
   • validation of de novo variants
     • computational e.g. calculate the probability of the mutation to be present in a family trio
     • experimental e.g. SANGER sequencing
   • clinical impact of de novo varints (UCSC Genome Browser)