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How to estimate and visualize haplotype blocks on a phased VCF/BCF

I am trying to split whole chromosome haplotypes or haplotypes in long phase blocks on common recombination points to haplotype blocks that can go into downstream analysis.

See also here for information about haplotype blocks.

https://www.broadinstitute.org/understanding-blocks

https://www.broadinstitute.org/haploview/blocks-and-haplotypes

Are HaploView and Plink still the best tools to do this? HaploView has not been developed/maintained for many years. Plink I never know which version to use, and I am not very familiar with the Plink data formats. And both don't work direct on phased VCF/BCF files.

Is there any recent/maintained tool that can estimate and visualize haplotype blocks, preferable interactively and using phased VCF/BCF as input? And can deal with large VCF/BCF files (in number of samples and variants)?

haplotype vcf
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updated by cmdcolin cmdcolin • written by William William

Did you happen to find a tool you liked? I just asked this question myself! :D

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written by draccident • draccident

No, this seems to be a neglected/forgotten area of bio-informatics (as mentioned in related question here on biostars).

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written by William William

1 answer

I recently created some tools for rendering phased VCF in the lastest version of jbrowse 2

It is a little "low level" since it's just the snp's instead of larger haplotype block chunks, but if you know what tools can generate the larger chunks we might be able to accommodate it

Here are a short tutorial with some screenshots https://jbrowse.org/jb2/docs/user_guides/analyze_trio/

Let me know if you have any feedback

enter image description here

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written by cmdcolin cmdcolin

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