This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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 ?