This is a tool used internally at the HudsonAlpha Institute for Biotechnology and is presented for the purposes of publication. It has not been designed to be portable outside of the HudsonAlpha compute cluster, so use elsewhere will require customization.
Given a BED file and either a bed file of genomic regions or VCF of structural variant calls, use IGV in headless mode to make graphs.
Cluster location: /cluster/lab/gcooper/igv-grapher
Given coordinates and BAM / BED / GFF and other IGV-viewable files, graph_region.sh calls IGV and saves a jpg image in the current working directory.
graph_bed.py loops through a BED file and for each interval saves a jpg image in the current working directory.
graph_vcf.py loops through a VCF and for each variant entry saves a pdf image with a (1) graph of the entire variant, (2) for variants > 1kb, graphs of each endpoint, and (3) information from the VCF record (ex: genotypes, INFO field, etc.). graph_vcf.py is optimized for use with structural variant VCFs, and has special handling for different SVTypes. BND events are plotted with both breakpoints; TRA events are skipped; etc. Despite being optimized for use with pbsv structural variant VCFs, most generic VCFs ought to work as well. hg38 is used by default but users may specify the path to another IGV genome.
For graph_bed.py and graph_vcf.py, users may add the --bsub flag to submit commands via LSF in parallel. The --print flag may be added to print commands instead of running them.
Primary use in Greg Cooper Lab: graphing structural variants from pacbio sequencing.
Note that the python files have #! instructions to use the virtual environment at /cluster/home/jlawlor/envs/igvgraph/ so the script should not be called using the python command, and using a version of python such as module load g/python/3.6.0 will likely cause conflicts. If this occurs, module unload any currently-loaded python installations.
$ /cluster/lab/gcooper/igv-grapher/graph_vcf.py -h
usage: graph_vcf.py [-h] -v VCF -b BAMS [BAMS ...] [-g GENOME] [-p PREFIX] [-s SLOP] [-k BREAKPOINT_SLOP] [-n INDEL_BP_THRESHOLD] [-w MAX_WIDTH] [--print] [--bsub]
Use IGV to graph BED regions
optional arguments:
-h, --help show this help message and exit
-v VCF, --vcf VCF VCF input filename
-b BAMS [BAMS ...], --bams BAMS [BAMS ...]
BAMS
-g GENOME, --genome GENOME
Genome (hg19 or hg38)
-p PREFIX, --prefix PREFIX
File prefix.
-s SLOP, --slop SLOP Slop: Number of bases to add at beginning and end of full graph
-k BREAKPOINT_SLOP, --breakpoint-slop BREAKPOINT_SLOP
Number of bases to add at beginning and end of breakpoint graph
-n INDEL_BP_THRESHOLD, --indel-bp-threshold INDEL_BP_THRESHOLD
Hide indels below this length.
-w MAX_WIDTH, --max-width MAX_WIDTH
Largest width event to graph at once. (MB). Above this size will only graph breakpoints
--print Print commands instead of executing them
--bsub Submit via LSF to default queue with recommended resources.
$ /cluster/lab/gcooper/igv-grapher/graph_bed.py -h
usage: graph_bed.py [-h] -r BED [-t TITLE] -b BAMS [BAMS ...] [-g GENOME] [-p PREFIX] [-s SLOP] [-n INDEL_BP_THRESHOLD] [--print] [--bsub]
Use IGV to graph BED regions. Location:/cluster/lab/gcooper/igv-grapher
optional arguments:
-h, --help show this help message and exit
-r BED, --bed BED BED input filename
-t TITLE, --title TITLE
BED title column
-b BAMS [BAMS ...], --bams BAMS [BAMS ...]
BAMS
-g GENOME, --genome GENOME
Genome (hg19 or hg38)
-p PREFIX, --prefix PREFIX
File prefix.
-s SLOP, --slop SLOP Slop: Number of bases to add at beginning and end of graph
-n INDEL_BP_THRESHOLD, --indel-bp-threshold INDEL_BP_THRESHOLD
Hide indels below this length.
--print Print commands instead of executing them
--bsub use bsub.
$ /cluster/lab/gcooper/igv-grapher/graph_region.sh -h
/cluster/lab/gcooper/igv-grapher/graph_region.sh -b BAM_PATH [-b BAM_PATH] [-v expand|squish|collapse] -r REGION [-c CHROMOSOME] [-s START] [-e END] -o OUTPUT_FILENAME [-n MIN_INDEL_TO_SHOW] [-g GENOME] ..
09/03/2021: Significant modification of graph_vcf.py to make multi-graph PDFs instead of a JPG. Update IGV version to 2.11.0.