Hi,

I am trying to build a pipeline for detecting de novo mutations for trios WES data.
After obtaining the VCF file, and performing all the possible recalibration and refinement steps, I reached this step where I have to phase my variants.

As I have understood, please correct me if the following is wrong:

1- phasing means relating the genotypes to their paternal and maternal origin

2- The de novo mutations will not be phased, because they violate the mendelian law of inheritance

3- PhaseByTransmission can be used to do this job perfectly: i.e. to phase varinats and find denovos

Thanks in advance
1) There are two common types of phasing: phasing by pedigree (by relating the alleles to the paternal or maternal origin via allele transmission), or local phasing (by determining which variants are locally in phase with each other, either by something like read backed phasing, or variant callers that directly call local haplotypes).

2) The de novo mutations can not be directly phased by pedigree, but they can be locally phased with respect to nearby variants (which may themselves be phased by pedigree).

3) You could use PhaseByTransmission, but you will obtain a better overall result if you jointly call the family using a pedigree-aware variant caller, such as `rtg family` or (for larger pedigrees) `rtg population` from [RTG Core][1]. This is because the pedigree-aware joint calling allows the evidence for each of the samples to influence the calls in other members of the pedigree (in `rtg population`, you can even use this to impute genotypes for missing family members during calling, which gets better the more family members you have). These callers automatically phase the output variants according to the pedigree, and directly output VCF annotations indicating putative de novo variants (including a de novo specific score).

(RTG Core also includes the `rtg mendelian` command which is useful for annotating VCFs for mendelian inheritance errors etc, and this command is also present in the smaller utility package [RTG Tools][2]). Disclaimer: I work for RTG :-).


  [1]: https://github.com/RealTimeGenomics/rtg-core
  [2]: https://github.com/RealTimeGenomics/rtg-tools