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Selection scans (Drosophila DGRP)

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.13. Desktop beta builds are coming soon.

In Drosophila melanogaster, a selective sweep at the insecticide-resistance gene Cyp6g1 (Daborn et al. 2002) and the In(2L)t inversion on chromosome 2L each leave a mark in population-genetic statistics: π dips at the sweep and Fst rises across the inversion. The inversion flips a stretch of 2L end to end and suppresses recombination between the inverted and standard arrangements in a heterozygote (Corbett-Detig & Hartl 2012). From a multi-sample VCF of 205 inbred lines we compute three statistics per window:

  • Fst, how far apart two groups' allele frequencies sit
  • nucleotide diversity (π), how much sequences differ within a group
  • Tajima's D, below zero where rare variants are in excess, as after a sweep

We load each as a quantitative track on dm6, read the Cyp6g1 sweep against the genes, then read the inversion.

Prerequisites

  • a JBrowse to open them in: Desktop takes a local file by path, Web through Add track
  • curl
  • node, for the JBrowse CLI
  • vcftools, for the windowed statistics
  • bcftools, to read the VCF header and sample list
  • htslib (bgzip, tabix), to index the VCF built in the per-sample section
  • bedGraphToBigWig, to pack a bedGraph into a bigWig

On Debian/Ubuntu, apt install vcftools bcftools tabix curl covers everything but node and bedGraphToBigWig, a single static binary from UCSC. Homebrew has the first three tools (brew install vcftools bcftools htslib), and bioconda has all four.

Where the data comes from

The Drosophila Genetic Reference Panel (DGRP) has 205 inbred lines (Mackay et al. 2012), lifted to dm6. The build script fetches these files, so there is nothing to download by hand.

The dm6 assembly and gene track come from the hosted UCSC hub.

Building Fst, π and Tajima's D bigWigs with vcftools

DGRPool records each line's In(2L)t arrangement (Gardeux et al. 2023), harmonizing the typing of Huang et al. 2015: 0 for standard homozygotes, 2 for inverted and 1 for heterozygotes. build_dgrp_popgen.sh drops the heterozygotes and writes the two sample lists, one name per line, that vcftools takes for --weir-fst-pop and --keep. It also renames DGRPool's DGRP_021 to the VCF's DGRP-021. DGRPool types In(3R)Payne too, so the same grouping on that phenotype scans 3R.

Each scan is a vcftools run, an awk step that turns its table into a bedGraph, and a bedGraphToBigWig pack. Fst uses the Weir & Cockerham estimator1 (Weir & Cockerham 1984):

# chrom.sizes from the VCF header, so it uses the contig names of the scans
bcftools view -h dgrp2.vcf.gz |
  awk -F'[=,>]' '/^##contig/{print $3"\t"$5}' > dm6.chrom.sizes

# window equal to step, so windows tile the genome
vcftools --gzvcf dgrp2.vcf.gz \
  --weir-fst-pop In2Lt_INV.txt --weir-fst-pop In2Lt_STD.txt \
  --fst-window-size 2000 --fst-window-step 2000 --out fst_In2Lt
# BIN_START is 1-based here, hence -1
# negative Fst is an estimator artifact at low-differentiation sites; floor at 0
# $5 is WEIGHTED_FST, the ratio of summed variance components
# $6, MEAN_FST, averages per-site ratios and swings on a few uninformative sites
# BIN_END is the nominal window end, so the last window of a contig passes its
# end; clamp it, or bedGraphToBigWig refuses the whole file
awk -F'\t' 'NR==FNR{len[$1]=$2; next}
     FNR>1 && $5!="nan" && $5!="-nan" {
       v=$5+0; if (v<0) v=0
       end=$3; if (end>len[$1]) end=len[$1]
       if (end>$2-1) print $1"\t"($2-1)"\t"end"\t"v
     }' dm6.chrom.sizes fst_In2Lt.windowed.weir.fst |
  sort -k1,1 -k2,2n > fst_In2Lt.bedgraph
bedGraphToBigWig fst_In2Lt.bedgraph dm6.chrom.sizes fst_In2Lt.bw

Diversity is the same three steps with --window-pi 2000, reading $5 of pi_all.windowed.pi, with --keep restricting it to one arrangement:

vcftools --gzvcf dgrp2.vcf.gz --window-pi 2000 --out pi_all
vcftools --gzvcf dgrp2.vcf.gz --keep In2Lt_INV.txt --window-pi 2000 --out pi_INV

$4 of the same table is the called-variant count the figure below stacks under π, packed into a bigWig by the same awk and bedGraphToBigWig pair.

Tajima's D (Tajima 1989) reports BIN_START 0-based, so there is no -1 shift, and has no BIN_END, so the awk builds the window end before the clamp:

vcftools --gzvcf dgrp2.vcf.gz --TajimaD 2000 --out tajimad_all
# BIN_START is already 0-based, and there is no BIN_END
# build the end here and clamp it to the contig length
awk -F'\t' 'NR==FNR{len[$1]=$2; next}
     FNR>1 && $4!="nan" && $4!="-nan" {
       end=$2+2000; if (end>len[$1]) end=len[$1]
       if (end>$2) print $1"\t"$2"\t"end"\t"$4
     }' dm6.chrom.sizes tajimad_all.Tajima.D |
  sort -k1,1 -k2,2n > tajimad_all.bedgraph
bedGraphToBigWig tajimad_all.bedgraph dm6.chrom.sizes tajimad_all.bw

2 kb windows resolve a single-gene sweep like Cyp6g1; widen toward 5-10 kb for genome-wide overviews.

The bigWigs take contig names from the VCF header (2L, 2R, X, FlyBase style) while UCSC dm6 writes chr2L, and refname aliasing maps one to the other. A mismatch with no alias draws an empty track and raises no error.

The DGRP VCF holds variant sites only, so --window-pi counts every position missing from the file as invariant and callable, and a window that lost sites to filtering shows low diversity.2 Filtering also shifts the whole baseline of Tajima's D, so read D at a locus against the genome-wide background of the 205 lines.

Loading the scans in JBrowse

We load dm6 from UCSC, whose reference names the arms chr2L. The alias file maps them to the bare 2L the scans use:

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "dm6",
  "aliases": ["BDGP6"],
  "sequence": {
    "adapter": {
      "type": "TwoBitAdapter",
      "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit"
    }
  },
  "refNameAliases": {
    "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chromAlias.txt"
  }
}
jbrowse add-assembly https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit \
  --name dm6 \
  --alias BDGP6 \
  --refNameAliases https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chromAlias.txt

The gene track is UCSC's RefSeq annotation of dm6:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "dm6_ncbiRefSeq",
  "name": "NCBI RefSeq genes",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeq.gff.gz"
  }
}
jbrowse add-track https://jbrowse.org/ucsc/dm6/ncbiRefSeq.gff.gz \
  --trackId dm6_ncbiRefSeq \
  --name "NCBI RefSeq genes" \
  --assemblyNames dm6

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track... and, in Add a track from file or URL, enter:

  • Main file: https://jbrowse.org/ucsc/dm6/ncbiRefSeq.gff.gz

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: NCBI RefSeq genes
  • Assembly: dm6

Click Add.

Each scan is a quantitative track over its bigWig. To load your own, swap uri for the bigWig your build wrote, whose contig names must match the assembly or its aliases.

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "fst_in2lt",
  "name": "Fst (In(2L)t vs standard, 2kb windows)",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
  }
}
jbrowse add-track https://jbrowse.org/demos/popgen/fst_In2Lt.bw \
  --trackId fst_in2lt \
  --name "Fst (In(2L)t vs standard, 2kb windows)" \
  --assemblyNames dm6

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track... and, in Add a track from file or URL, enter:

  • Main file: https://jbrowse.org/demos/popgen/fst_In2Lt.bw

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: Fst (In(2L)t vs standard, 2kb windows)
  • Assembly: dm6

Click Add.

Fst and π are on different scales, so each gets a track and a y-axis. A multi-wiggle track shares one axis across rows, which suits one statistic across groups, so the per-group π bigWigs load as one track:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "MultiQuantitativeTrack",
  "trackId": "pi_by_arrangement",
  "name": "π by In(2L)t arrangement",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "π In(2L)t",
        "uri": "https://jbrowse.org/demos/popgen/pi_INV.bw"
      },
      {
        "type": "BigWigAdapter",
        "source": "π standard",
        "uri": "https://jbrowse.org/demos/popgen/pi_STD.bw"
      }
    ]
  }
}
jbrowse add-track-json '{
  "type": "MultiQuantitativeTrack",
  "trackId": "pi_by_arrangement",
  "name": "π by In(2L)t arrangement",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "π In(2L)t",
        "uri": "https://jbrowse.org/demos/popgen/pi_INV.bw"
      },
      {
        "type": "BigWigAdapter",
        "source": "π standard",
        "uri": "https://jbrowse.org/demos/popgen/pi_STD.bw"
      }
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "MultiQuantitativeTrack",
  "trackId": "pi_by_arrangement",
  "name": "π by In(2L)t arrangement",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "MultiWiggleAdapter",
    "subadapters": [
      {
        "type": "BigWigAdapter",
        "source": "π In(2L)t",
        "uri": "https://jbrowse.org/demos/popgen/pi_INV.bw"
      },
      {
        "type": "BigWigAdapter",
        "source": "π standard",
        "uri": "https://jbrowse.org/demos/popgen/pi_STD.bw"
      }
    ]
  }
}

Each arrangement's π swings several fold between 2 kb windows, far more than the two arrangements differ, so two rows of it look alike. Pooling into 250 kb bins and taking log2 of inverted over standard gives one track that sits at zero where the arrangements have equal diversity. An awk step writes it from the two π bedGraphs:

# B: bin width; each bin's pi is the length-weighted mean of its 2 kb windows
awk -F'\t' -v OFS='\t' -v B=250000 '
  NR==FNR { len[$1]=$2; next }
  FNR==1 { g++ }
  { k=$1 SUBSEP int($2/B); w=$3-$2; s[g,k]+=$4*w; n[g,k]+=w; seen[k] }
  END {
    for (k in seen) if (s[1,k]>0 && s[2,k]>0) {
      split(k, a, SUBSEP); end=(a[2]+1)*B; if (end>len[a[1]]) end=len[a[1]]
      print a[1], a[2]*B, end, log((s[1,k]/n[1,k])/(s[2,k]/n[2,k]))/log(2)
    }
  }' dm6.chrom.sizes pi_INV.bedgraph pi_STD.bedgraph |
  sort -k1,1 -k2,2n > pi_ratio_In2Lt.bedgraph
bedGraphToBigWig pi_ratio_In2Lt.bedgraph dm6.chrom.sizes pi_ratio_In2Lt.bw

In grammar-of-graphics terms, color is a color scale: a field mapped through a domain to a range of colors. Here a threshold scale colors each bin by its side of zero, and scales.y pins the y scale to ±1.5:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "pi_ratio_in2lt",
  "name": "π, In(2L)t over standard (log2, 250 kb bins)",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/pi_ratio_In2Lt.bw"
  },
  "displayDefaults": {
    "color": {
      "field": "score",
      "scale": "threshold",
      "domain": [0],
      "range": ["#e66100", "#1f78b4"],
      "labels": ["inverted lower", "inverted higher"],
      "title": "π, In(2L)t vs standard"
    },
    "scales": {
      "y": { "domainMin": -1.5, "domainMax": 1.5, "title": "log2 ratio" }
    }
  }
}
jbrowse add-track https://jbrowse.org/demos/popgen/pi_ratio_In2Lt.bw \
  --trackId pi_ratio_in2lt \
  --name "π, In(2L)t over standard (log2, 250 kb bins)" \
  --assemblyNames dm6 \
  --displayDefaults '{"color":{"field":"score","scale":"threshold","domain":[0],"range":["#e66100","#1f78b4"],"labels":["inverted lower","inverted higher"],"title":"π, In(2L)t vs standard"},"scales":{"y":{"domainMin":-1.5,"domainMax":1.5,"title":"log2 ratio"}}}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "QuantitativeTrack",
  "trackId": "pi_ratio_in2lt",
  "name": "π, In(2L)t over standard (log2, 250 kb bins)",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/pi_ratio_In2Lt.bw"
  },
  "displayDefaults": {
    "color": {
      "field": "score",
      "scale": "threshold",
      "domain": [0],
      "range": ["#e66100", "#1f78b4"],
      "labels": ["inverted lower", "inverted higher"],
      "title": "π, In(2L)t vs standard"
    },
    "scales": {
      "y": { "domainMin": -1.5, "domainMax": 1.5, "title": "log2 ratio" }
    }
  }
}

Advanced → Edit plot... in the track menu shows color and scales as text and applies edits live.

Reading the Cyp6g1 sweep in Tajima's D and π

Search Cyp6g1 in the location box and add three QuantitativeTracks shaped like the Fst track above, each over all 205 lines: Tajima's D, π, and the called-variant count per window (column 4 of the table π comes from).

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "tajd_all",
  "name": "Tajima's D (whole panel)",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/tajimad_all.bw"
  }
}
jbrowse add-track https://jbrowse.org/demos/popgen/tajimad_all.bw \
  --trackId tajd_all \
  --name "Tajima's D (whole panel)" \
  --assemblyNames dm6

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track... and, in Add a track from file or URL, enter:

  • Main file: https://jbrowse.org/demos/popgen/tajimad_all.bw

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: Tajima's D (whole panel)
  • Assembly: dm6

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "pi_all",
  "name": "π (whole panel)",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/pi_all.bw"
  }
}
jbrowse add-track https://jbrowse.org/demos/popgen/pi_all.bw \
  --trackId pi_all \
  --name "π (whole panel)" \
  --assemblyNames dm6

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track... and, in Add a track from file or URL, enter:

  • Main file: https://jbrowse.org/demos/popgen/pi_all.bw

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: π (whole panel)
  • Assembly: dm6

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

Goes in the tracks array of config.json. See Tracks.

{
  "type": "QuantitativeTrack",
  "trackId": "sites_all",
  "name": "Called variants per window",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "BigWigAdapter",
    "uri": "https://jbrowse.org/demos/popgen/sites_all.bw"
  }
}
jbrowse add-track https://jbrowse.org/demos/popgen/sites_all.bw \
  --trackId sites_all \
  --name "Called variants per window" \
  --assemblyNames dm6

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track... and, in Add a track from file or URL, enter:

  • Main file: https://jbrowse.org/demos/popgen/sites_all.bw

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: Called variants per window
  • Assembly: dm6

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

To band the swept window, drag across chr2R:12,130,000-12,200,000 on the scalebar and pick Highlight region.

Tajima's D, π and called variants per window across 2R around Cyp6g1 (highlighted; Cyp6g1 and Cyp6g2 labeled in the gene track). D and π dip together over the highlighted window against their background either side, and the count of called variants under them falls with them.
Open in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fucsc%2Fdm6%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22tajd_all%22%2C%22name%22%3A%22Tajima%27s+D+%28whole+panel%29%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Ftajimad_all.bw%22%7D%7D%2C%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22pi_all%22%2C%22name%22%3A%22%CF%80+%28whole+panel%29%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fpi_all.bw%22%7D%7D%2C%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22sites_all%22%2C%22name%22%3A%22Called+variants+per+window%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Fsites_all.bw%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22dm6%22%2C%22loc%22%3A%22chr2R%3A12%2C000%2C000-12%2C400%2C000%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr2R%22%2C%22start%22%3A12130000%2C%22end%22%3A12200000%2C%22assemblyName%22%3A%22dm6%22%2C%22label%22%3A%22Cyp6g1%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22tajd_all%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A150%7D%2C%7B%22trackId%22%3A%22pi_all%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A120%7D%2C%7B%22trackId%22%3A%22sites_all%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A100%7D%2C%7B%22trackId%22%3A%22dm6-ncbiRefSeqCurated%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A115%2C%22showOnlyGenes%22%3Atrue%2C%22featureHighlights%22%3A%5B%7B%22refName%22%3A%22chr2R%22%2C%22name%22%3A%22Cyp6g1%22%7D%2C%7B%22refName%22%3A%22chr2R%22%2C%22name%22%3A%22Cyp6g2%22%7D%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+popgen%2Ftajimad_cyp6g1

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses dm6, loaded from a .2bit genome.
  2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a BigWig file (.bw).This figure uses “Tajima's D (whole panel)”.
  3. Add the next track the same way. This one needs a BigWig file (.bw).This figure uses “π (whole panel)”.
  4. Add the next track the same way. This one needs a BigWig file (.bw).This figure uses “Called variants per window”.
  5. Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq - RefSeq Curated”.
    1. Track menu → Show only genes (checked)
    2. Right-click the feature → Highlight feature (searching for it by name in the location box leaves the same highlight behind)This figure highlights 2 features. The spec form differs from the click in one way that matters to a figure: a highlight the user did not click also sorts its feature to a top row of the track, so it is boxed at the top of a dense lane rather than boxed several rows down.
  6. Type your region of interest into the location box and press Enter.This figure is at chr2R:12,000,000-12,400,000.
  7. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track https://jbrowse.org/demos/popgen/tajimad_all.bw \
  --trackId tajd_all \
  --name "Tajima's D (whole panel)" \
  --assemblyNames dm6

jbrowse add-track https://jbrowse.org/demos/popgen/pi_all.bw \
  --trackId pi_all \
  --name "π (whole panel)" \
  --assemblyNames dm6

jbrowse add-track https://jbrowse.org/demos/popgen/sites_all.bw \
  --trackId sites_all \
  --name "Called variants per window" \
  --assemblyNames dm6

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs dm6 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/ucsc/dm6/config.json, which is what the Web button above opens.

{
  "sessionTracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "tajd_all",
      "name": "Tajima's D (whole panel)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/tajimad_all.bw"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "pi_all",
      "name": "π (whole panel)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/pi_all.bw"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "sites_all",
      "name": "Called variants per window",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/sites_all.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "loc": "chr2R:12,000,000-12,400,000",
      "highlight": [
        {
          "refName": "chr2R",
          "start": 12130000,
          "end": 12200000,
          "assemblyName": "dm6",
          "label": "Cyp6g1"
        }
      ],
      "tracks": [
        {
          "trackId": "tajd_all",
          "type": "LinearWiggleDisplay",
          "height": 150
        },
        {
          "trackId": "pi_all",
          "type": "LinearWiggleDisplay",
          "height": 120
        },
        {
          "trackId": "sites_all",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "dm6-ncbiRefSeqCurated",
          "type": "LinearBasicDisplay",
          "height": 115,
          "showOnlyGenes": true,
          "featureHighlights": [
            {
              "refName": "chr2R",
              "name": "Cyp6g1"
            },
            {
              "refName": "chr2R",
              "name": "Cyp6g2"
            }
          ]
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/dm6/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "QuantitativeTrack",
            "trackId": "tajd_all",
            "name": "Tajima's D (whole panel)",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "uri": "https://jbrowse.org/demos/popgen/tajimad_all.bw"
            }
        },
        {
            "type": "QuantitativeTrack",
            "trackId": "pi_all",
            "name": "π (whole panel)",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "uri": "https://jbrowse.org/demos/popgen/pi_all.bw"
            }
        },
        {
            "type": "QuantitativeTrack",
            "trackId": "sites_all",
            "name": "Called variants per window",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "uri": "https://jbrowse.org/demos/popgen/sites_all.bw"
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "dm6",
            "loc": "chr2R:12,000,000-12,400,000",
            "highlight": [
                {
                    "refName": "chr2R",
                    "start": 12130000,
                    "end": 12200000,
                    "assemblyName": "dm6",
                    "label": "Cyp6g1"
                }
            ],
            "tracks": [
                {
                    "trackId": "tajd_all",
                    "type": "LinearWiggleDisplay",
                    "height": 150
                },
                {
                    "trackId": "pi_all",
                    "type": "LinearWiggleDisplay",
                    "height": 120
                },
                {
                    "trackId": "sites_all",
                    "type": "LinearWiggleDisplay",
                    "height": 100
                },
                {
                    "trackId": "dm6-ncbiRefSeqCurated",
                    "type": "LinearBasicDisplay",
                    "height": 115,
                    "showOnlyGenes": True,
                    "featureHighlights": [
                        {
                            "refName": "chr2R",
                            "name": "Cyp6g1"
                        },
                        {
                            "refName": "chr2R",
                            "name": "Cyp6g2"
                        }
                    ]
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

cat > tracks.json <<'JSON'
[
  {
    "type": "QuantitativeTrack",
    "trackId": "tajd_all",
    "name": "Tajima's D (whole panel)",
    "assemblyNames": [
      "dm6"
    ],
    "adapter": {
      "type": "BigWigAdapter",
      "uri": "https://jbrowse.org/demos/popgen/tajimad_all.bw"
    }
  },
  {
    "type": "QuantitativeTrack",
    "trackId": "pi_all",
    "name": "π (whole panel)",
    "assemblyNames": [
      "dm6"
    ],
    "adapter": {
      "type": "BigWigAdapter",
      "uri": "https://jbrowse.org/demos/popgen/pi_all.bw"
    }
  },
  {
    "type": "QuantitativeTrack",
    "trackId": "sites_all",
    "name": "Called variants per window",
    "assemblyNames": [
      "dm6"
    ],
    "adapter": {
      "type": "BigWigAdapter",
      "uri": "https://jbrowse.org/demos/popgen/sites_all.bw"
    }
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/ucsc/dm6/config.json \
  --tracks tracks.json \
  --assembly dm6 --loc chr2R:12,000,000-12,400,000 \
  --track tajd_all display:LinearWiggleDisplay '{"height":150}' \
  --track pi_all display:LinearWiggleDisplay '{"height":120}' \
  --track sites_all display:LinearWiggleDisplay '{"height":100}' \
  --track dm6-ncbiRefSeqCurated display:LinearBasicDisplay '{"height":115,"showOnlyGenes":true,"featureHighlights":[{"refName":"chr2R","name":"Cyp6g1"},{"refName":"chr2R","name":"Cyp6g2"}]}' \
  --width 1500 --out figure.svg

It has no flag for this figure's highlight, so its picture can differ there.

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "tajd_all",
      "name": "Tajima's D (whole panel)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/tajimad_all.bw"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "pi_all",
      "name": "π (whole panel)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/pi_all.bw"
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "sites_all",
      "name": "Called variants per window",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/sites_all.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "loc": "chr2R:12,000,000-12,400,000",
      "highlight": [
        {
          "refName": "chr2R",
          "start": 12130000,
          "end": 12200000,
          "assemblyName": "dm6",
          "label": "Cyp6g1"
        }
      ],
      "tracks": [
        {
          "trackId": "tajd_all",
          "type": "LinearWiggleDisplay",
          "height": 150
        },
        {
          "trackId": "pi_all",
          "type": "LinearWiggleDisplay",
          "height": 120
        },
        {
          "trackId": "sites_all",
          "type": "LinearWiggleDisplay",
          "height": 100
        },
        {
          "trackId": "dm6-ncbiRefSeqCurated",
          "type": "LinearBasicDisplay",
          "height": 115,
          "showOnlyGenes": true,
          "featureHighlights": [
            {
              "refName": "chr2R",
              "name": "Cyp6g1"
            },
            {
              "refName": "chr2R",
              "name": "Cyp6g2"
            }
          ]
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "anchor": {
      "trackId": "tajd_all",
      "loc": "chr2R:12,008,000",
      "fracY": 0.63,
      "alignX": "left"
    },
    "text": "Cyp6g1, insecticide resistance. Tajima's D and π both\nfall against the flanking windows: a recent hard sweep.",
    "fontSize": 15,
    "maxWidth": 440
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/dm6/config.json \
  --width 1500 --height 810 \
  --timeout 90000 \
  --spec session.json --annotations callouts.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Called variants fall under the sweep because a duplication of Cyp6g1 segregates alongside the resistance allele (Schmidt et al. 2010), and the duplicated sequence lowers the number of sites called in the window.

The In(2L)t inversion, genome-wide and within each arrangement

Open the assembly with no location to lay the six arms out side by side, with the In(2L)t Fst track across all of them.

The inversion itself is one <INV> record spanning the published breakpoints, genotyped 1/1 in the inverted lines and 0/0 in the standard ones. The END field holds the far breakpoint:

#CHROM  POS      ID     REF  ALT    QUAL  FILTER  INFO                     FORMAT  DGRP-026  DGRP-032
2L      2225744  In2Lt  N    <INV>  .     PASS    SVTYPE=INV;END=13154180  GT      1/1       0/0

The samples TSV pairs each line with its karyotype (standard or inverted). In grammar-of-graphics terms, facet splits the display into sections, one per karyotype value, facet.domain orders them, and rowColor is a color scale on each row's label bar:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "VariantTrack",
  "trackId": "dgrp_In2Lt_sv",
  "name": "In(2L)t inversion genotyped across DGRP lines",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_sv.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "facet": { "field": "karyotype", "domain": ["Standard", "In(2L)t"] },
      "rowColor": "karyotype"
    }
  ]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "dgrp_In2Lt_sv",
  "name": "In(2L)t inversion genotyped across DGRP lines",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_sv.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "facet": { "field": "karyotype", "domain": ["Standard", "In(2L)t"] },
      "rowColor": "karyotype"
    }
  ]
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "dgrp_In2Lt_sv",
  "name": "In(2L)t inversion genotyped across DGRP lines",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_sv.vcf.gz",
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/demos/popgen/dgrp_In2Lt_samples.tsv"
    }
  },
  "displays": [
    {
      "type": "LinearMultiSampleVariantDisplay",
      "facet": { "field": "karyotype", "domain": ["Standard", "In(2L)t"] },
      "rowColor": "karyotype"
    }
  ]
}

The track above Fst in the figure marks the published extent with one inline feature:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "in2lt_inversion",
  "name": "In(2L)t inversion",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "uniqueId": "in2lt",
        "refName": "chr2L",
        "start": 2225744,
        "end": 13154180,
        "name": "In(2L)t"
      }
    ]
  }
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "in2lt_inversion",
  "name": "In(2L)t inversion",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "uniqueId": "in2lt",
        "refName": "chr2L",
        "start": 2225744,
        "end": 13154180,
        "name": "In(2L)t"
      }
    ]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "FeatureTrack",
  "trackId": "in2lt_inversion",
  "name": "In(2L)t inversion",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "uniqueId": "in2lt",
        "refName": "chr2L",
        "start": 2225744,
        "end": 13154180,
        "name": "In(2L)t"
      }
    ]
  }
}

Open chr2L alone, with the π ratio track under Fst:

Top: the six dm6 arms with the In(2L)t extent over Fst between the two arrangements; the block on 2L stands against low background elsewhere. Below, chr2L alone with π in the inverted lines over π in the standard ones, log2 in 250 kb bins.
Open in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fucsc%2Fdm6%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22in2lt_inversion%22%2C%22name%22%3A%22In%282L%29t+inversion%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22adapterId%22%3A%22in2lt%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22in2lt%22%2C%22refName%22%3A%22chr2L%22%2C%22start%22%3A2225744%2C%22end%22%3A13154180%2C%22name%22%3A%22In%282L%29t%22%2C%22type%22%3A%22inversion%22%7D%5D%7D%7D%2C%7B%22type%22%3A%22QuantitativeTrack%22%2C%22trackId%22%3A%22fst_in2lt%22%2C%22name%22%3A%22Fst+%28In%282L%29t+vs+standard%2C+2kb+windows%29%22%2C%22assemblyNames%22%3A%5B%22dm6%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22BigWigAdapter%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fpopgen%2Ffst_In2Lt.bw%22%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22dm6%22%2C%22displayedRegionNames%22%3A%5B%22chr2L%22%2C%22chr2R%22%2C%22chr3L%22%2C%22chr3R%22%2C%22chr4%22%2C%22chrX%22%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22in2lt_inversion%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22height%22%3A40%7D%2C%7B%22trackId%22%3A%22fst_in2lt%22%2C%22type%22%3A%22LinearWiggleDisplay%22%2C%22height%22%3A240%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+popgen%2Ffst_in2lt_2L

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses dm6, loaded from a .2bit genome.
  2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs features defined inline in the config.This figure uses “In(2L)t inversion”.
  3. Add the next track the same way. This one needs a BigWig file (.bw).This figure uses “Fst (In(2L)t vs standard, 2kb windows)”.

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "in2lt_inversion",
  "name": "In(2L)t inversion",
  "assemblyNames": [
    "dm6"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "adapterId": "in2lt",
    "features": [
      {
        "uniqueId": "in2lt",
        "refName": "chr2L",
        "start": 2225744,
        "end": 13154180,
        "name": "In(2L)t",
        "type": "inversion"
      }
    ]
  }
}'

jbrowse add-track https://jbrowse.org/demos/popgen/fst_In2Lt.bw \
  --trackId fst_in2lt \
  --name "Fst (In(2L)t vs standard, 2kb windows)" \
  --assemblyNames dm6

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs dm6 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Spec tab, or jbrowse set-default-session.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/ucsc/dm6/config.json, which is what the Web button above opens.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "in2lt_inversion",
      "name": "In(2L)t inversion",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "in2lt",
        "features": [
          {
            "uniqueId": "in2lt",
            "refName": "chr2L",
            "start": 2225744,
            "end": 13154180,
            "name": "In(2L)t",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "fst_in2lt",
      "name": "Fst (In(2L)t vs standard, 2kb windows)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "displayedRegionNames": [
        "chr2L",
        "chr2R",
        "chr3L",
        "chr3R",
        "chr4",
        "chrX"
      ],
      "tracks": [
        {
          "trackId": "in2lt_inversion",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "type": "LinearWiggleDisplay",
          "height": 240
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/ucsc/dm6/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "in2lt_inversion",
            "name": "In(2L)t inversion",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "adapterId": "in2lt",
                "features": [
                    {
                        "uniqueId": "in2lt",
                        "refName": "chr2L",
                        "start": 2225744,
                        "end": 13154180,
                        "name": "In(2L)t",
                        "type": "inversion"
                    }
                ]
            }
        },
        {
            "type": "QuantitativeTrack",
            "trackId": "fst_in2lt",
            "name": "Fst (In(2L)t vs standard, 2kb windows)",
            "assemblyNames": [
                "dm6"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "dm6",
            "displayedRegionNames": [
                "chr2L",
                "chr2R",
                "chr3L",
                "chr3R",
                "chr4",
                "chrX"
            ],
            "tracks": [
                {
                    "trackId": "in2lt_inversion",
                    "type": "LinearBasicDisplay",
                    "height": 40
                },
                {
                    "trackId": "fst_in2lt",
                    "type": "LinearWiggleDisplay",
                    "height": 240
                }
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "in2lt_inversion",
      "name": "In(2L)t inversion",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "adapterId": "in2lt",
        "features": [
          {
            "uniqueId": "in2lt",
            "refName": "chr2L",
            "start": 2225744,
            "end": 13154180,
            "name": "In(2L)t",
            "type": "inversion"
          }
        ]
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "fst_in2lt",
      "name": "Fst (In(2L)t vs standard, 2kb windows)",
      "assemblyNames": [
        "dm6"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://jbrowse.org/demos/popgen/fst_In2Lt.bw"
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "dm6",
      "displayedRegionNames": [
        "chr2L",
        "chr2R",
        "chr3L",
        "chr3R",
        "chr4",
        "chrX"
      ],
      "tracks": [
        {
          "trackId": "in2lt_inversion",
          "type": "LinearBasicDisplay",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "type": "LinearWiggleDisplay",
          "height": 240
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/ucsc/dm6/config.json \
  --width 1500 --height 560 \
  --timeout 90000 \
  --spec session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The inverted lines have less diversity than the standard ones across the inverted region, most near the breakpoints, where the suppressed recombination is strongest. Toward the centromere past the inversion, where the arrangements recombine freely, the ratio sits at zero. Differentiation decays gradually outside the breakpoints (Corbett-Detig & Hartl).

Reproduce it end to end

build_dgrp_popgen.sh wraps every step above and writes a ready-to-serve config:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_dgrp_popgen.sh
bash build_dgrp_popgen.sh                  # builds ./dgrp_popgen_build/jbrowse2
npx --yes serve dgrp_popgen_build/jbrowse2 # then open the printed URL

The config opens on In(2L)t across arm 2L. The .bw and .vcf.gz files are written next to it, to host elsewhere or open as local track files in JBrowse Desktop.

See also

Citations

Notes

  1. The inverted and standard groups are very unequal in size, since the inverted arrangement is the rarer one. Hudson's estimator is the usual recommendation where groups differ this much (Bhatia et al. 2013); A selected haplotype (Dog10K) scans with that one. ↩

  2. pixy (Korunes & Samuk 2021) takes an allSites VCF and reports π, dxy and Fst per window without that bias, and its output packs into a bigWig the same way. ↩