Homozygosity graph - improvements

[davmlaw]

🤖 Written by Claude

Moved from a private issue, originally raised by @TheMadBug. @davmlaw gave explicit permission to move this particular issue after manually checking that it contained no private information.

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A said:

An adjustable window size might be a useful feature -- that way you can 
leave it to the user to decide on resolution, which can be based on their prior 
knowledge of gene-density (and their exome capture kit).

A more serious version of this would be to plot gene density as a  separate track under each chromosome, and/or have a zoom feature......

Another suggestion A had was to use the thickness of the bar to indicate the number of SNPs in the bin. That gives us an extra dimension over colour.

Comments from the original issue

@TheMadBug wrote:

Actually, I meant use the thickness to indicate gene density, not number of SNPs in the bin…..that way regions with low gene density
don’t show up as homozygous. The way to define gene density would be (# of bases in exons/# number of bases in some window) — that
way exon length is factored in.

@davmlaw wrote:

L says the LOH graph is a tease at the moment as you can only see it from a very far distance.

Ideas for improvements:
-Adjustable bin size
-Be able to obtain areas where there are runs of homozygosity
-Maybe be able to find out how far away the nearest HET snp is?
-Image map tag to jump to "sort to that bin?" http://www.w3schools.com/tags/tag_map.asp

We are using 1mb bin size, which gives us only a bit over 3k for a whole genome (and much less for exomes etc) so maybe this is achievable for a Plotly graph

@davmlaw wrote:

Detecting Runs of Homozygosity in Ancient DNA - https://www.biorxiv.org/content/10.1101/2020.05.31.126912v2

@davmlaw wrote:

Someone had this as their feedback feature request.

It would also be good to annotate a VCF with how far the next het site is, so you can see how big a hom run is?

@sksmi wrote:

Maybe address at the same time as looking at peddy & LOH tools? The graph is cool, but prob need details to do a proper analysis and can be addressed external to VG for the time-being.