Load by ID

Load by allele support

No allele selected
Click an allele in the flow view to find its carriers
0 alleles selected
1 Evidence
2 Strategy
3 Count · up to 0 eligible
1
4 Preview · loading 0 of 0 eligible

Grouping

Add a Variable above to list participant groups.
Display
ThemeT Auto
OrientationO Horizontal
Variant LayoutV Genomic
Full screenF Enter full screen
Interaction
Lock viewport
Click chromosome to jump
Alleles
Lock allele positions
Aggregate low-frequency
Cutoff %
Maintenance
Local cache Clear

Tracks

UCSC Tracks

Genes

Variants

Comments

Help

Genomeshader is an interactive browser for population-scale genetic variation. Instead of paging through one sample at a time, you explore a whole cohort at once — the goal is to see which variants matter and who carries them.

The core idea
You navigate primarily between variants. Each variant is shown with its alleles and how frequently they occur across the cohort. When a variant looks interesting, you deep-dive into the sample cohort from it — pulling up the reads of the samples that carry a given allele to see the underlying evidence.
Legend
Reference bases — A green, C blue, G orange, T red (IGV-style, colored blocks with contrast letters at deep zoom).
Reference allele — the ref allele band; width scales with how many samples carry it.
Alternate allele (SNV) — a single-base variant allele.
Insertion — labelled INS in the tooltip. Click its marker on the Indel track to expand the inserted bases in place.
Deletion — labelled DEL. Click its Indel-track marker to grey out the deleted reference bases.
No-call (./.) — genotype missing for that sample.
Deleted span — greyed, struck-through reference bases when a deletion is expanded.
Indel-track marker — a position with an insertion or deletion; click to expand it.
Comment pin — a comment anchored to this locus; click to open it in the Comments tab.
Typical workflow
  1. Scan variants. Move along the genome; the variant track marks each site and the flow ("alleuvial") display shows each allele as a band sized by its frequency in the cohort.
  2. Pick an allele. Click an allele band to select it, or double-click it to open both side panels at once — samples on the left, the variant's details on the right (Variants tab). Rare alleles can be folded together (Settings → Alleles) so common structure stands out.
  3. Deep-dive the cohort. Load samples carrying that allele as read tracks ("Smart Tracks"). A loading strategy decides which samples to pull first (e.g. a random draw, or the best-evidence carriers).
  4. Inspect the evidence. Reads render on the GPU with strand direction and per-base coloring against the reference so you can confirm the call.
Moving around
  • Pan: drag the main view left/right.
  • Zoom: scroll or pinch.
  • Lock viewport: the padlock in the locus bar, or Settings → Lock viewport, freezes pan and zoom. Go and chromosome-click jump still work.
  • Jump: load a specific sample by ID from the Sample Search box in the left panel (press ↓ for the list).
  • Select / reorder alleles: click an allele band to select; drag bands to reorder them.
  • Deep-dive a variant: double-click an allele band to open both side panels — sample selection on the left, variant details on the right.
  • Inspect indels: click an insertion/indel marker to expand it in place and read the inserted bases; click again to collapse it.
Tracks
  • Chromosome overview — the ideogram in the top locus bar; it shows the whole contig, not the current window.
  • Reference — the reference sequence as IGV-style colored bases, with a genomic ruler.
  • Genes — the union of overlapping transcripts.
  • Variants + flow — variant sites and their allele frequencies across the cohort.
  • Reads — reads for the samples you've pulled in.

Collapse any track with its ▼ / ▶ button; a minimized track stays as a labeled bar you can click to expand. Either side panel collapses via the protruding tab on its inner edge.

Left panel tabs
  • Samples — two independent paths: Load by ID, or Load by allele support (Evidence → Strategy → Count → Preview → Load).
  • Groups — add one or more metadata Variables (AND filters) and color the flow by one of them.
  • Settings — display, allele, and interaction options.
Right panel tabs
  • Tracks — rename, show/hide, collapse, and reorder every track in the display (including Smart Tracks loaded from alleles). The gear on each row opens track-specific options (read tracks can show mates as pairs).
  • Genes — descriptions of the genes currently in view.
  • Variants — details for the selected variant; the ◀ ▶ arrows at the top step between variants, and a second pair steps between that variant's alleles (changing the selection). When a Grouping Variable is set, a per-group sample-frequency chart appears for the selected allele(s).
Keyboard shortcuts
  • F — full screen
  • T — cycle theme (auto / light / dark)
  • O — orientation (horizontal / vertical)
  • V — variant layout (equidistant / to-scale)