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Display phasing in VCFs

asked 2019-12-18 16:25:34 -0600

J M gravatar image

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?



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answered 2019-12-18 16:30:21 -0600

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

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Thanks for the quick reply! Is this project open source? If so, I could see trying to contribute this feature myself. If not, please let me know when there is such a capability!

J M ( 2019-12-18 16:51:54 -0600 )edit
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Asked: 2019-12-18 16:25:34 -0600

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Last updated: Dec 18 '19