Hey there,
When I load a VCF into GenomeBrowser, it nicely displays all my variants for all my samples. However, if I load a VCF with phased haplotypes and Sample1 has genotype 0|1 at Variant1 and 2|0 at Variant2 (a multiallelic variant), then it seems that Sample1 is displayed as 0|1, 0|2 in the browser, not 0|1, 2|0. Is there any option that, for phased VCFs, will force alleles in the same row for a sample to always be of the same haplotype?
Thanks,
Jonathan
Hi Jonathan,
Currently GenomeBrowse will always display a heterogeneous genotype (regardless of phase) in the orientation of the reference on the top and the alternate on the bottom.
I see the appeal of being able to visualize the phase orientation, and it would probably warrant a slightly different display mode. But there is no current option to take the phase information into account.
Thanks, Gabe
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2019-12-18 16:25:34 -0600
Seen: 2,681 times
Last updated: Dec 18 '19
