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What is the best way to find denovo mutations in trios?
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 thins workflow is efficient and best 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 ?