Images

GW can generate static images in .png/.pdf format of target genomic regions. These can be saved to a file but only .png images can be re-opened for exploring at a later date. Images can be generated using the snapshot command, or using options on the command line.

The command line options are detailed below.

Saving images

Images are directed to stdout, to a file using the -f option, or to a folder using --outdir. The --no-show/-n option is also needed to stop GW displaying a window:

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 saved to file

All variants in a VCF file can also be generated:

gw hg38.fa -b your.bam -v variants.vcf --outdir all_images -n -t 16

Or, all chromosome in a BAM file can be drawn:

gw t2t -t 12 -b your.bam -n --outdir chrom_plots

GW can also encode the genomic location of a region in the file name, allowing you to open static images alongside bam files at a later date. To use this function, let GW name the png file for you by supplying only the output directory with --outdir:

gw hg38.fa -b your.bam -r chr1:1-20000 --outdir . -n

Here an image file will be saved in the current directory with the filename GW~chr1~1~20000~.png.

Opening images

The image file mentioned above can be opened alongside a BAM file, allowing you to explore the image dynamically:

gw hg19 -i GW~chr1~1~20000~.png -b your.bam

Images saved in .png format can be opened in a similar way to variant data, using the -i or –images option. Files are input using a glob pattern. For example all .png images in a folder called ‘images’ can be opened with:

gw -i "images/*.png"

If you previously used GW to generate images from a vcf file (see example in Variant data section), any parsed-labels will be saved in the –outdir directory. For example if –outdir images was used when generating images, you can now view these images and labels using:

gw -i "images/*.png" --in-labels images/gw.parsed_labels.tsv

To open one or more bam files alongside your images you will need to supply a reference genome. Right-clicking using the mouse will then switch between images and bam files:

gw hg38.fa -b your.bam -i "images/*.png"