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

Merged
merged 17 commits into from
Dec 7, 2024
Merged

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

merged 17 commits into from
Dec 7, 2024

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cmdcolin
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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
@cmdcolin
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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

@cmdcolin cmdcolin force-pushed the variant_matrix branch 9 times, most recently from af98fbb to f4f87f1 Compare December 7, 2024 05:29
@cmdcolin cmdcolin force-pushed the variant_matrix branch 2 times, most recently from b206629 to c91c544 Compare December 7, 2024 07:10
@cmdcolin cmdcolin marked this pull request as ready for review December 7, 2024 07:13
@cmdcolin cmdcolin changed the title Add multi-sample 'matrix' display for multi-sample VCFs Add 'matrix' display for multi-sample VCFs Dec 7, 2024
@cmdcolin cmdcolin merged commit 3ed4ac6 into main Dec 7, 2024
@cmdcolin cmdcolin deleted the variant_matrix branch December 7, 2024 07:28
@cmdcolin cmdcolin added the enhancement New feature or request label Dec 10, 2024
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