Entering edit mode
9 weeks ago
safeassli
▴
10
Hello, I'm currently looking to phase my normalized vcf file. It's worth noting that I'm working with non-human organisms and utilizing reference gene sequences.
I've previously experimented with WhatsHap; however, I observed that it doesn't phase genotypes labeled as 0/0. Considering this limitation, I'm exploring alternative tools for phasing. I'm uncertain whether Beagle would be suitable for my specific case. Any suggestions or insights on alternative tools would be greatly appreciated. Thank you!
How could such a genotype even be phased?
Sprry but I'm not an expert in this field. I'm trying to learn Only 0/1, 1/0, and 1/1 genotypes should be phased, as these indicate the presence of the alternative allele ?