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:

1. Alignment to reference genome
2. marking duplicates
3. base recalibration
4. realigning indels
5. Haplotype caller per sample with the -ERC GVCF option (this will call the ReadBackedPhasing, correct?)
6. Joint genotyping
7. Varinat recalibration

8. 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!

Many thanks