Questions tagged [phasing]

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Genotyping technologies do not maintain phase?

Why exactly does genotyping not maintain phase? I guess I'm more confused on what's the difference between sequencing and genotyping, and as a result how phase is maintained in one, but not the other. ...
5
votes
1answer
85 views

Searching tool to calculate phase/switch error rate

I'm looking for a tool which, given a truth vcf file and a test vcf file, calculates the phase/switch error rate. I performed phasing of a vcf using WhatsHap and want to compare the outcome to some ...
2
votes
2answers
80 views

Using Beagle 4.1 for phasing and IBD - chromosomes

I am trying to use beagle 4.1 for phasing and IBD analyses. I was wondering if I need to run the analysis by chromosome or I can put them together in the same vcf file.