GW

GW is a fast browser for genomic sequencing data (.bam/.cram format) used directly from the terminal. GW also allows you to view and annotate variants from vcf/bcf files.

Check out the documentation here.

⚙️ Install

For best performance, download one of the app packages from the Releases page. See the install section of the documentation for more details.

Using a package manager:

• brew (Apple or Linux):

brew install kcleal/homebrew-gw/gw

• conda (x86_64 Apple or Linux)

conda install -c bioconda -c conda-forge gw

Unfortunatly the Linux conda package is not currently working for miniconda/miniforge, altough other distributions may work. To build from source using conda to fetch other dependencies use:

conda create -y -n gw_env -c conda-forge glfw htslib
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

🚀 Quick Start

Command line:

# Start gw (drag and drop bams into window)
gw hg38

# 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/LABEL
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
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

Here are a few GW commands (others are available). Access command box with : or /:

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

Sequencing data

To view a genomic region e.g. chr1:1-20000, supply an indexed reference genome and an alignment file (using -b option):

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

Variant data

A variant file in .vcf/.bcf format can be opened in a GW window by either dragging-and-dropping or via the -v option:

gw hg38.fa -b your.bam -v variants.vcf

Benchmark

See test directory.

Issues and contributing

If you find bugs, or have feature requests please open an issue, or drop me an email clealk@cardiff.ac.uk. GW is under active development, and we would welcome any contributions!