I recommed checking out igv-reports which has more features and active development before attempting to use this IGV-snapshot-automator.
Also check out BamSnap for IGV-like bam file visualization; https://github.com/parklab/bamsnap
The features of this IGV-snapshot-automator are entirely limited to commands that can be used in IGV batch script;
A script to automatically create and run IGV snapshot batchscripts. This script will first write an IGV batch script for the supplied input files, then load all supplied files for visualization (.bam, etc) in a headless IGV session and take snapshots at the locations defined in the regions.bed file.
Designed for use on Linux systems, and intended to be used as a component of sequencing analysis pipelines.
Use the included Makefile recipe to download a copy of IGV
make install
-
Put your chromosome regions to visualize in the
regions.bedfile (provided), or another BED format file -
Locate your files to visualize (e.g. .bam & .bam.bai files)
-
Create and run batchscript. Example command:
$ python make_IGV_snapshots.py /path/to/alignments1.bam /path/to/alignments2.bamTo run the script on the included demo files:
$ python make_IGV_snapshots.py test_data/test_alignments.bam test_data/test_alignments2.bamSee python make_IGV_snapshots.py --help for available options. Here are a few:
-r: Path to the BED formatted regions file to use (defaults to the included demoregions.bed)-nosnap: Make batchscript without taking snapshots-g: Genome to use, e.g.hg19-ht: Height of the snapshot, default is 500-o: Name of the output directory to save the snapshots in (defaults toIGV_Snapshots)-bin: Path to the IGV jar binary to run (defaults toigv.jar)-mem: Memory to allocate to IGV (MB)-suffix: Filename suffix to place before '.png' in the snapshots-onlysnap: Skip batchscript creation and only run IGV using the supplied batchscript file-nf4: "Name field 4" mode, uses values saved in 4th field of theregions.bedfile as the output filename of the PNG snapshot. Use this when you have pre-made filenames you wish to use for each snapshot.-sor-group_by_strand: Group alignment(s) by read strand with forward on top and reverse on the bottom.
Default memory allotment is set at 4GB; this can be changed with the -mem argument (e.g. -mem 1000 sets memory to 1GB).
IGV may take several minutes to run, depending on the number of input files and regions to snapshot. Stdout messages from the program may not appear immediately in the console.
Docker and Singularity container files are included. Pre built container images can be found on Dockerhub at https://hub.docker.com/repository/docker/stevekm/igv-snapshot-automator
The Docker container can be built with the included Makefile recipe
make docker-build
The test data can be run with
make docker-test
The Singularity container can be built using Docker with the included Makefile recipe
make singularity-build
The test data can be run with
make singularity-test
- Python 2.7 or 3+
- bash version 4.1.2+
- IGV (download script provided in
bindirectory) - Xvfb
- xdpyinfo
- Java runtime environment
- Docker or Singularity for building and running containers
Some alternative implementations of the same basic methodology used here for creating IGV snapshots can also be found implemented in Nextflow pipelines;
Running a batch script on IGV:
Details on interpretation of IGV visualizations can be found here:
IGV available preferences which could be included in IGV batch scripts:
igv-reports which makes HTML report outputs with embedded Javascript IGV viewer