Skip to main content

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.20. Desktop beta builds for Linux and macOS are on the releases page; the Windows build waits on code signing.

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 windowed population-genetic statistics. π (diversity within a group) dips at the sweep and Tajima's D falls below zero there, while Fst (the distance between two groups' allele frequencies) 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). Starting from a multi-sample VCF of inbred lines and vcftools' windowed statistics, packed into bigWigs, we:

  • load the Fst bigWig as a quantitative track on dm6 beside the genes
  • add Tajima's D, π and called-variant tracks at Cyp6g1 and highlight the sweep
  • open all six arms with the inversion's extent over Fst
  • stack π for each arrangement in a multi-wiggle track, then color a log2 ratio track with a threshold scale
  • facet a one-record inversion VCF into karyotype sections from a sample sheet

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
# Debian/Ubuntu
sudo apt install samtools bcftools tabix vcftools nodejs
# or conda, which has every tool above
conda install -c bioconda -c conda-forge samtools bcftools htslib vcftools \
  nodejs ucsc-bedgraphtobigwig
# or Linux x86_64 binaries for the tools apt lacks
wget -P ~/.local/bin \
  https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
chmod +x ~/.local/bin/bedGraphToBigWig
# any platform
npm install -g @jbrowse/cli@next

The data

The Drosophila Genetic Reference Panel (DGRP) has 205 inbred lines (Mackay et al. 2012), lifted to dm6. You don't need these files to follow the page: the track configs below read the hosted results. The build script fetches them to rebuild those results. The vcftools steps take your own VCF and two sample lists.

What it isFile
The DGRP freeze-2 genotype callsDGRP2.source_NCSU.dm6.final.SNPs_only.vcf.gz
The In(2L)t inversion karyotype for each line, from DGRPool's phenotype recorddownload

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, since it removes the rare alleles D is most sensitive to, and vcftools counts two chromosomes where an inbred line contributes one. Read D at a locus against the genome-wide background of all the 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 curated RefSeq annotation of dm6:

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

{
  "type": "FeatureTrack",
  "trackId": "dm6-ncbiRefSeqCurated",
  "name": "NCBI RefSeq - RefSeq Curated",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz"
    },
    "index": {
      "indexType": "CSI",
      "location": {
        "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz.csi"
      }
    }
  }
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "dm6-ncbiRefSeqCurated",
  "name": "NCBI RefSeq - RefSeq Curated",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz"
    },
    "index": {
      "indexType": "CSI",
      "location": {
        "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz.csi"
      }
    }
  }
}'

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": "dm6-ncbiRefSeqCurated",
  "name": "NCBI RefSeq - RefSeq Curated",
  "assemblyNames": ["dm6"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz"
    },
    "index": {
      "indexType": "CSI",
      "location": {
        "uri": "https://jbrowse.org/ucsc/dm6/ncbiRefSeqCurated.gff.gz.csi"
      }
    }
  }
}

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.

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 the 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 ↗

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 ↗

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 ↗

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, Cyp6g1 highlighted.
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open new genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses dm6, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs a BigWig file (.bw).This figure uses “Tajima's D (whole panel)”.
  3. Add the next track the same way. Needs a BigWig file (.bw).This figure uses “π (whole panel)”.
  4. Add the next track the same way. Needs a BigWig file (.bw).This figure uses “Called variants per window”.
  5. Add the next track the same way. Needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq - RefSeq Curated”.
    1. Track menu → Filter by → Genes → Only genesGenes counts every gene, transcript and RNA type, the configured transcript and container types, and a top-level CDS; the rest of a GFF, such as NCBI region and match rows, is not a gene.
    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. Go to your region in the location box.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.

Paste into a coding agent, with your goal on the first line.

My goal: [write yours, e.g. this view of my own files, or these track settings in my config.json]

Start from this JBrowse view.
- Config it loads: https://jbrowse.org/ucsc/dm6/config.json
- Tracks:
  - Tajima's D (whole panel) (tajd_all), QuantitativeTrack, a BigWig file (.bw), drawn as LinearWiggleDisplay
  - π (whole panel) (pi_all), QuantitativeTrack, a BigWig file (.bw), drawn as LinearWiggleDisplay
  - Called variants per window (sites_all), QuantitativeTrack, a BigWig file (.bw), drawn as LinearWiggleDisplay
  - NCBI RefSeq - RefSeq Curated (dm6-ncbiRefSeqCurated), FeatureTrack, a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi), drawn as LinearBasicDisplay

Docs: https://jbrowse.org/jb2/docs/agents_authoring/ (writing a config), https://jbrowse.org/jb2/docs/agents/ (driving a running JBrowse). Use the jbrowse-authoring, jbrowse-hosted-data and jbrowse-capture skills if you have them. Check any config with `npx @jbrowse/cli validate`, then render it and look: a config that loads is not yet a track that drew.

The session spec that draws the view:
{
  "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",
          "height": 150
        },
        {
          "trackId": "pi_all",
          "height": 120
        },
        {
          "trackId": "sites_all",
          "height": 100
        },
        {
          "trackId": "dm6-ncbiRefSeqCurated",
          "height": 115,
          "filter": [
            "geneLike"
          ],
          "featureHighlights": [
            {
              "refName": "chr2R",
              "name": "Cyp6g1"
            },
            {
              "refName": "chr2R",
              "name": "Cyp6g2"
            }
          ]
        }
      ]
    }
  ]
}
Redraw the figure headlessly
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",
          "height": 150
        },
        {
          "trackId": "pi_all",
          "height": 120
        },
        {
          "trackId": "sites_all",
          "height": 100
        },
        {
          "trackId": "dm6-ncbiRefSeqCurated",
          "height": 115,
          "filter": [
            "geneLike"
          ],
          "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

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file (replace YOUR_FILE).

jbrowse add-track https://jbrowse.org/demos/popgen/tajimad_all.bw \
  --trackId tajd_all \
  --name "Tajima's D (whole panel)" \
  --assemblyNames dm6 \
  --displayDefaults '{"height":150}'

jbrowse add-track https://jbrowse.org/demos/popgen/pi_all.bw \
  --trackId pi_all \
  --name "π (whole panel)" \
  --assemblyNames dm6 \
  --displayDefaults '{"height":120}'

jbrowse add-track https://jbrowse.org/demos/popgen/sites_all.bw \
  --trackId sites_all \
  --name "Called variants per window" \
  --assemblyNames dm6 \
  --displayDefaults '{"height":100}'

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "dm6-ncbiRefSeqCurated",
  "name": "NCBI RefSeq - RefSeq Curated",
  "assemblyNames": [
    "dm6"
  ],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "YOUR_FILE"
  },
  "displayDefaults": {
    "height": 115,
    "filter": [
      "geneLike"
    ]
  }
}'

Run beside config.json, or add --out <dir>. Needs dm6 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your 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",
                    "height": 150
                },
                {
                    "trackId": "pi_all",
                    "height": 120
                },
                {
                    "trackId": "sites_all",
                    "height": 100
                },
                {
                    "trackId": "dm6-ncbiRefSeqCurated",
                    "height": 115,
                    "filter": [
                        "geneLike"
                    ],
                    "featureHighlights": [
                        {
                            "refName": "chr2R",
                            "name": "Cyp6g1"
                        },
                        {
                            "refName": "chr2R",
                            "name": "Cyp6g2"
                        }
                    ]
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws this view as an SVG, no browser needed. Swap --config or a track for your own.

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 \
  --view '{"highlight":[{"refName":"chr2R","start":12130000,"end":12200000,"assemblyName":"dm6","label":"Cyp6g1"}]}' \
  --track tajd_all '{"height":150}' \
  --track pi_all '{"height":120}' \
  --track sites_all '{"height":100}' \
  --track dm6-ncbiRefSeqCurated '{"height":115,"filter":["geneLike"],"featureHighlights":[{"refName":"chr2R","name":"Cyp6g1"},{"refName":"chr2R","name":"Cyp6g2"}]}' \
  --width 1500 --out figure.svg

For a PNG, --out figure.png (needs rsvg-convert: apt install librsvg2-bin, brew install librsvg).

The session spec behind the figure, over this config.

{
  "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",
          "height": 150
        },
        {
          "trackId": "pi_all",
          "height": 120
        },
        {
          "trackId": "sites_all",
          "height": 100
        },
        {
          "trackId": "dm6-ncbiRefSeqCurated",
          "height": 115,
          "filter": [
            "geneLike"
          ],
          "featureHighlights": [
            {
              "refName": "chr2R",
              "name": "Cyp6g1"
            },
            {
              "refName": "chr2R",
              "name": "Cyp6g2"
            }
          ]
        }
      ]
    }
  ]
}

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. A track above Fst marks the published extent of the inversion 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"
      }
    ]
  }
}

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 π bigWig of each arrangement loads as one row of a single 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 the two rows look alike. Pool into 250 kb bins and take log2 of inverted over standard to get 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, encoding.color is a color scale: the score mapped through scale.domain to a scale.range of colors. Here a threshold scale colors each bin by its side of zero, and encoding.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": {
    "encoding": {
      "y": {
        "scale": { "domainMin": -1.5, "domainMax": 1.5 },
        "axis": { "title": "log2 ratio" }
      },
      "color": {
        "scale": {
          "type": "threshold",
          "domain": [0],
          "range": ["#e66100", "#1f78b4"],
          "names": ["inverted lower", "inverted higher"]
        },
        "legend": { "title": "π, In(2L)t vs standard" }
      }
    }
  }
}
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 '{"encoding":{"y":{"scale":{"domainMin":-1.5,"domainMax":1.5},"axis":{"title":"log2 ratio"}},"color":{"scale":{"type":"threshold","domain":[0],"range":["#e66100","#1f78b4"],"names":["inverted lower","inverted higher"]},"legend":{"title":"π, In(2L)t vs standard"}}}}'

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": {
    "encoding": {
      "y": {
        "scale": { "domainMin": -1.5, "domainMax": 1.5 },
        "axis": { "title": "log2 ratio" }
      },
      "color": {
        "scale": {
          "type": "threshold",
          "domain": [0],
          "range": ["#e66100", "#1f78b4"],
          "names": ["inverted lower", "inverted higher"]
        },
        "legend": { "title": "π, In(2L)t vs standard" }
      }
    }
  }
}

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

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

Top: the six dm6 arms with the In(2L)t extent over Fst. Below: chr2L with the log2 π ratio of inverted over standard lines.
Open in JBrowse Web ↗

Or rebuild it from your own data:

Quickest: open the view, then File → Open track... for your files.

From scratch:

  1. Open your genome: Open new genome in JBrowse Desktop, or jbrowse add-assembly for JBrowse Web.This figure uses dm6, loaded from a .2bit genome.
  2. Add your track: File → Open track..., or check it in the track selector. Needs features defined inline in the config.This figure uses “In(2L)t inversion”.
  3. Add the next track the same way. Needs a BigWig file (.bw).This figure uses “Fst (In(2L)t vs standard, 2kb windows)”.

Paste into a coding agent, with your goal on the first line.

My goal: [write yours, e.g. this view of my own files, or these track settings in my config.json]

Start from this JBrowse view.
- Config it loads: https://jbrowse.org/ucsc/dm6/config.json
- Tracks:
  - In(2L)t inversion (in2lt_inversion), FeatureTrack, features defined inline in the config, drawn as LinearBasicDisplay
  - Fst (In(2L)t vs standard, 2kb windows) (fst_in2lt), QuantitativeTrack, a BigWig file (.bw), drawn as LinearWiggleDisplay

Docs: https://jbrowse.org/jb2/docs/agents_authoring/ (writing a config), https://jbrowse.org/jb2/docs/agents/ (driving a running JBrowse). Use the jbrowse-authoring, jbrowse-hosted-data and jbrowse-capture skills if you have them. Check any config with `npx @jbrowse/cli validate`, then render it and look: a config that loads is not yet a track that drew.

The session spec that draws the view:
{
  "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",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "height": 240
        }
      ]
    }
  ]
}
Redraw the figure headlessly
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",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "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

More: Using JBrowse with AI agents.

Adds these tracks to your config.json, styled as in the figure. Point each uri at your file.

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"
      }
    ]
  },
  "displayDefaults": {
    "height": 40
  }
}'

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 \
  --displayDefaults '{"height":240}'

Run beside config.json, or add --out <dir>. Needs dm6 in the config (jbrowse add-assembly).

This view in a notebook, with jbrowse-anywidget. Swap a track's uri for your 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",
                    "height": 40
                },
                {
                    "trackId": "fst_in2lt",
                    "height": 240
                }
            ]
        }
    ],
)
app  # display the widget

The session spec behind the figure, over this config.

{
  "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",
          "height": 40
        },
        {
          "trackId": "fst_in2lt",
          "height": 240
        }
      ]
    }
  ]
}

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).

Genotyping the inversion in each line

The karyotype that split the lines into two groups also loads as a track, one row per line. The inversion is one <INV> record spanning the published breakpoints, genotyped 1/1 in the inverted lines and 0/0 in the standard ones, with the far breakpoint in END:

#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). facet splits the display into sections, one per karyotype value, facet.sort orders them, and rows.color 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": "LinearVariantDisplay",
      "facet": { "field": "karyotype", "sort": ["Standard", "In(2L)t"] },
      "rows": { "color": "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": "LinearVariantDisplay",
      "facet": { "field": "karyotype", "sort": ["Standard", "In(2L)t"] },
      "rows": { "color": "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": "LinearVariantDisplay",
      "facet": { "field": "karyotype", "sort": ["Standard", "In(2L)t"] },
      "rows": { "color": "karyotype" }
    }
  ]
}

With a sample sheet of your own, name any of its columns in facet to split the rows by it. Grouping and ordering shows this track under the Fst scan.

Reproduce it end to end

build_dgrp_popgen.sh wraps every step above. The script:

  1. Downloads the DGRP2 dm6 SNP VCF and the In(2L)t karyotypes.
  2. Splits the lines into inverted and standard groups, and writes Fst, π, their inverted-over-standard ratio and Tajima's D as bigWigs over windows with vcftools.
  3. Builds the one-record inversion VCF that genotypes every line.
  4. Downloads JBrowse and writes a config.json with dm6 and every track, opening on In(2L)t.
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. ↩