How to estimate and visualize haplotype blocks on a phased VCF/BCF
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12 weeks ago
William ★ 5.1k

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

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

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