Entering edit mode
2.3 years ago
Sarah
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60
Hello, I am trying to phase a VCF file for a non-model organism that has no reference panel. I have a VCF file of genotypes for 30 samples from various populations of a species, which I phased using read-based phasing with Whatshap. This managed to phase about 75% of my heterozygous sites, but a downstream analyses requires all heterozygous sites to be phased. Is there a method that can phase just the unphased sites/genotypes in my VCF, without disrupting the existing phasing? From the documentation, it seems like Beagle would treat the entire VCF as unphased and undo my read-based phasing. Thank you!
Unfortunately if you don't have a reference panel it's not really possible to phase only 30 samples - the results would be very unreliable with that few samples.