Images and tiles

Variant image tiles

Load a variant file (VCF/BCF/BED/GW_LABEL) and each variant is drawn as a static image tile. Scroll with the mouse or arrow keys.

Load by drag-and-drop, the load command, or --var/-v. Dragged VCF/BCF files become tiles or a track depending on vcf_as_tracks (Settings → Interaction).

Screenshot placeholder — tiled variant images
docs/assets/images/v2/tiles.png

• Right-click a tile to switch to the interactive alignment view; right-click again to return
• Left-click a tile to cycle its label
• Multiple variant files: the rectangles at top-left show the current file — click another to switch (or COMMAND/CTRL + →)

gw hg19 -b HG002.bwa.bam -v variants1.vcf -v variants2.vcf

VCF files can be streamed through bcftools:

bcftools view -r chr1:1-1000000 your.bcf | gw hg38 -b your.bam -v -

Static images from the command line

gw hg38 -b your.bam -r chr1:1-20000 -n > out.png                 # png to stdout
gw hg38 -b your.bam -r chr1:1-20000 -n --fmt pdf -f out.pdf       # pdf
gw t2t -t 24 -b your.bam -n --outdir chrom_plots                  # every chromosome, parallel
gw hg38.fa -b your.bam -v variants.vcf --outdir all_images --no-show -t 16

Output options: --dims, --theme (igv, dark, slate), --font-size, --ylim, --cov, --ideogram, --fmt, -f/--outdir.

Screenshots

snapshot (alias s) saves a PNG of the current view.