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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 |
cross posted: https://www.biostars.org/p/279970/
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