Phasing with Beagle 5.2 and no reference panel

Phasing with Beagle 5.2 and no reference panel

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Hi everyone,

I have a question about phasing with Beagle 5.2 without a reference panel. I have seen in answers in a couple other posts about Beagle that trying to phase with too few samples and no reference panel is not advised. I was wondering if anyone had any insights into what constitutes “too few samples”? Or any suggestions where I could go to learn more about this? I have a multi-sample vcf file with 24 samples that I generated with GATK HaplotypeCaller that I was hoping to phase, but I do not have a reference panel. After looking into this I am now wondering if I have too few samples for this analysis.

I would really appreciate any insights you may have!
Thank you


Beagle


Phase

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