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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.A

    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 ?

    Many thanks

  • #2
    cross posted: https://www.biostars.org/p/279970/

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