Phasing in Trios for unique clinical presentation

Question

[zephryin]

Hello,

I am fairly new to analyzing trios data. The study design consists of WGS on an affected proband with a rare clinical presentation. I figured out my filtering pipeline but I am wondering if I should also be looking at phasing. As far as I understand, phasing shouldn't tell me anymore information than my filtering given that I have probands with unique presentations. Am I correct? If not, can you guide me to a place that would describe it in more detail? Thanks!

Answer 1

[Vivek]

I don't see how phasing is redundant with filtering. From the GATK publications I've read they claim that the genotyper's likelihood estimates are accurate for 85% of the variants. However you could generate a higher accuracy with a phasing tool.

Answer 2

[zephryin]

So if I am understanding you correctly, that would mean that the initial variant calls would be more accurate if I were to use a phasing tool? What if I were just looking for de novo? Would using it still be useful?

[Vivek]

Certainly, the higher your accuracy of parental haplotype determination, the better your chances of characterizing a mutation as a de novo in the offspring. There's software like DenovoGear & GATK's PhaseByTransmission which do that.