Quick Start

Desktop Application:

When you start GW for the first time you will see a prompt with a list of online reference genomes - select an appropriate genome tag from the list by typing in a number. You can update this list from the main menu when GW has loaded.

Once a reference genome has been loaded, drag-and-drop data files such as bam or bed’s into the graphical window. The command box can be accessed by pressing the forward-slash key /, or by clicking on the bubble towards the left-hand-side of the screen. Navigate to a region by typing, for example /chr2.

For further help on command usage, see the help menu by typing /help, or for detailed manuals type /man COMMAND, where COMMAND is the name of the command in question. More information is available in the Commands section of the User Guide.

GW also supports opening a bam file by double-clicking. In order for this to work, a matching reference genome is needed in the GW configuration file, see the Settings section for more details.

Command line:

Start gw using the hg38 genome tag, next, drag and drop bams into the window:

gw hg38

Open a target bam file (a matching reference genome will be needed in the config file):

gw a.bam

View start of chr1:

gw hg38 -b your.bam -r chr1:

Two regions, side-by-side:

gw hg38 -b your.bam -r chr1:1-20000 -r chr2:50000-60000

Multiple bams:

gw hg38 -b '*.bam' -r chr1
gw hg38 -b b1.bam -b b2.bam -r chr1

Add a track BED/VCF/BCF/GFF3/GTF/GW_LABEL/BIGBED/BIGWIG:

gw hg38 -b your.bam -r chr1 --track a.bed

png image to stdout:

gw hg38 -b your.bam -r chr1:1-20000 -n > out.png

Save pdf:

gw hg38 -b your.bam -r chr1:1-20000 -n --fmt pdf -f out.pdf

Plot every chromosome in parallel:

gw t2t -t 24 -b your.bam -n --outdir chrom_plots

View VCF/BCF/BED as tiled images:

gw hg38 -b your.bam -v var.vcf

View VCF/BCF from stdin:

gw hg38 -b your.bam -v -

View some png images:

gw -i "images/*.png"

Save some annotations:

gw hg38 -b your.bam -v var.vcf --labels Yes,No --out-labels labels.tsv

Useful commands

GW commands - access command box with : or /. Example commands:

help              # help menu
config            # open config file for editing
chr1:1-20000      # Navigate to region
add chr2:1-50000  # Append new region
rm 1              # Region at column index 1 removed
rm bam1           # Bam file at row index 1 removed
mate              # Move view to mate of read
mate add          # mate added in new view
line              # Toggle vertical line
ylim 100          # View depth increased to 100
find QNAME        # Highlight all reads with qname==QNAME
filter mapq >= 10 # Filer reads for mapq >= 10
count             # Counts of all reads for each view point
snapshot          # Save screenshot to .png
man COMMAND       # manual for command