Quickstart
1. Build GW
GW v2 is in beta and must be built from source — see Installation for platform details:
conda create -y -n gw_env -c conda-forge glfw htslib ncurses
conda activate gw_env
git clone https://github.com/kcleal/gw.git
cd gw && make prep
CONDA_PREFIX=$(conda info --base) LDLIBS+="-lcrypto -lssl" make -j4
2. Launch GW and pick a genome
gw
A terminal picker lists the online reference genomes — type a number or a tag such as hg38. To skip the picker, pass the tag on the command line (gw hg38). Genomes can also be added later in Settings → Genomes — local FASTA files are much faster than online genomes.
3. Open data
Drag-and-drop a BAM/CRAM into the window. GW opens it and navigates to the first chromosome. Add more files the same way: further BAMs stack vertically, tracks (BED/VCF/GFF/GTF/bigBed/bigWig) appear below the alignments.
To browse and download remote data without leaving GW, use the Online files dialog from the top menu — it includes online genomes, data catalogues and a UCSC table search.
4. The interface
- Plot window — click a read to select it, right-click for its popup, drag to zoom, scroll to zoom at the cursor
- Top menu — hamburger button (top-left): open files, settings, save images/sessions, online files. The view dropdown controls layout options
- Command box — press
:or/, then type a command (below)
docs/assets/images/v2/quickstart_annotated.png See The interface for a full tour.
5. Useful commands
help # help menu
chr1:1-20000 # navigate to region
add chr2:1-50000 # append new region
rm 1 # remove region at column index 1
mate # move view to mate of read
find QNAME # highlight all reads with qname == QNAME
filter mapq >= 10 # filter reads
count # read counts for each view
snapshot # save screenshot
translate # translate reads
marker chr1:15000 # add a marker
man COMMAND # manual for COMMAND
See Commands for the full list.
Command line (power users)
Everything above can be scripted. Open files directly, split regions, generate images without a window:
gw hg38 -b your.bam -r chr1:1-20000
gw hg38 -b your.bam -r chr1:1-20000 -r chr2:50000-60000 # two regions side-by-side
gw hg38 -b b1.bam -b b2.bam -r chr1 # stacked bams
gw hg38 -b your.bam -v var.vcf # variant tiles
gw hg38 -b your.bam -r chr1 -c 'sort strand' # apply a command at launch
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
gw t2t -t 24 -b your.bam -n --outdir chrom_plots # every chromosome, in parallel
bcftools view -r chr1:1-1000000 your.bcf | gw hg38 -b your.bam -v -
All command-line options: gw --help.