I have around 100 trios for which WES was done. My goal is to find denovo mutations in the child associated with each trios. So first I will do the following steps:
- Alignment to reference genome
- marking duplicates
- base recalibration
- realigning indels
- Haplotype caller per sample with the -ERC GVCF option (this will call the ReadBackedPhasing, correct?)
- Joint genotyping
- Varinat recalibration
Genotype refinement workflow, where pedegree information is used and de novos are annotated using VariantAnnotator.
1- Do you think this workflow is efficient to find denovos?
2- Are the variants in the output vcf file produced after step 8 already phased ? (because ReadBackedPhasing was already used in step 5)
3- Do I need to use PhaseByTransmission afterwards after step 8 ?
Thanks for all your feedback!