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.
Please visit the install section of the documentation for more details, or download one of the binaries from the Releases page.
TLDR: conda install -c bioconda -c conda-forge gw
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
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
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
See test directory.
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!