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Misc Add phase set parsing Accomodate phase set (PS) with random colors Add potato demo
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Hello all! | ||
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This release announces v3.0.0 of JBrowse 2. Is not a dramatic change like the | ||
jbrowse 1 -> jbrowse 2 transition, it's much more incremental, and in fact, you | ||
can go on calling it JBrowse 2...as a point of comparison, ggplot2 is on v3.5.1 | ||
right now :) | ||
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We decided to make a major bump due to some small "breaking" changes that could | ||
affect plugin and embedded library users in particular. | ||
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But for most users, this release should have nothing but the usual bugfixes and | ||
improvements! And there are a lot of these! | ||
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Without further ado, here are some highlights! | ||
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## Improved rendering of phased VCF in multi-variant view | ||
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Phased variants offer a unique opportunity to see "which parent" particular | ||
parents came from | ||
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 | ||
Screenshot showing the "phased mode" for the multi-variant matrix display, here | ||
showing a "trio VCF" with child and parents. You can visually see which blocks | ||
the child inherited from which parents. This inspection can also be useful for | ||
plant breeders to ensure regions that their crosses inherited particular gnomic | ||
regions from a particular parent line | ||
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We can also render "phased sets" if the VCF is not completely phased (detects PS | ||
tag in genotypes) | ||
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 | ||
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Screenshot showing phase set rendering of a phased VCF. This is nearly | ||
completely phased so just showing green, but each phase set would get a unique | ||
color. The black entries are unphased variants (which could be filtered out, but | ||
this is not done currently) | ||
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## Improved rendering of polyploid VCF in multi-variant view | ||
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 | ||
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Screenshot showing the "polyploid" rendering of the multi-variant display. | ||
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Polyploid variant calls can look like `0/2/./1` indicating one match to the | ||
reference (0), two alts (1,2), and one missing call (.). | ||
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- Yellow indicates missingness | ||
- Grey indicates reference | ||
- Blue indicates the ALT===1 | ||
- Red is ALT!==1 | ||
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Each of these is a spectrum that increases in darkness, so darker blue indicates | ||
more ALT===1, darker red indicates more ALT!==1, darker yellow is more uncalled, | ||
etc. | ||
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## Adding VCF sample metadata from TSV | ||
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 | ||
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Screnshot showing multi-sample matrix display, with the population colors coming | ||
from a "sample TSV" file | ||
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Config | ||
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```json | ||
{ | ||
"type": "VariantTrack", | ||
"trackId": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf", | ||
"name": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf", | ||
"assemblyNames": ["hg19"], | ||
"adapter": { | ||
"type": "VcfTabixAdapter", | ||
"vcfGzLocation": { | ||
"uri": "https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | ||
}, | ||
"index": { | ||
"location": { | ||
"uri": "https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi" | ||
} | ||
}, | ||
"samplesTsvLocation": { | ||
"uri": "https://jbrowse.org/genomes/hg19/1000g.sorted.csv.gz" | ||
} | ||
} | ||
} | ||
``` | ||
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## Improved UI for opening synteny tracks | ||
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It has always been a little tricky to open synteny tracks | ||
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We now allow support adding synteny tracks via the default "Add track" workflow, | ||
and make it easier to specify the query and target assembly names | ||
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 | ||
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Screnshot showing the default add track workflow with new UI for choosing target | ||
and query assemblies for PAF tracks | ||
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 | ||
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Screenshot showing the add track workflow in the Linear synteny view import | ||
form, also showing new UI for choosing query and target assmblies | ||
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## New "turbo zoom" buttons | ||
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In working with users, we noticed people having to click the zoom buttons or | ||
fiddle with the slider a lot. To aid this, we added a small dropdown for quickly | ||
doing 10x, 50x, and 100x zooms | ||
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 | ||
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## For developers: some "breaking" changes | ||
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1. We changed the "filehandle" type used in data adapters. We now use | ||
generic-filehandle2 which is simpler and does not require a node.js polyfill | ||
on the web | ||
2. Upgrading React 18 -> React 19 in our main webapp. This drops support for | ||
React 17, and may have some other implications | ||
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If you are a plugin or embedded user, and experience problems with upgrading, | ||
let us know! |
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