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Add multi-sample 'matrix' display for multi-sample VCFs #4511

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@cmdcolin cmdcolin commented Aug 6, 2024

This is an older effort and is still in a bit under construction but could be useful to push forward

example image
image

potential todos

  • label rows
  • sort rows
  • group rows
  • draw line from matrix position to genomic position, or just draw the lines at actual genomic position (these two use cases have different purposes)
  • minor allele frequency filter to filter out low freq variants

functionality is similar to multivariantviewer (jb1 plugin) and igv

image

https://www.youtube.com/watch?v=ZKwm8dqIQpg

@cmdcolin cmdcolin marked this pull request as draft August 6, 2024 02:52
@cmdcolin cmdcolin force-pushed the variant_matrix branch 2 times, most recently from 550ed80 to a1cee86 Compare August 12, 2024 17:38
@cmdcolin cmdcolin force-pushed the variant_matrix branch 3 times, most recently from 608d7a2 to de2b6f4 Compare November 19, 2024 14:08
Updates

Small updates + minor allele frequency

[skip ci] Test

T1

T5

Bump yarn.lock

Fix some types

Update snap

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Add autogen docs

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Combined with some optimizations to vcf-js (GMOD/vcf-js#105) we can visualize large 500+kb regions of 1000 genomes dataset without too much trouble (example below takes ~10 seconds)

image

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