Introduction

A python package to generate and execute IGV screenshot script. Adapted from access-mpath-scripts

Setting up a Dev Environment

It is recommended to run this tool via the Docker container.

To set up the package locally for development purposes see the following steps.

Install External Dependencies

Create an environment with python >= 3.9, Java and IGV installed on path.

Generic Java Install:

wget https://download.java.net/openjdk/jdk11/ri/openjdk-11+28_linux-x64_bin.tar.gz
tar xvf openjdk-11+28_linux-x64_bin.tar.gz
export JAVA_HOME=/path/to/jdk-11
export PATH=$JAVA_HOME/bin:$PATH

Generic IGV install:

wget https://data.broadinstitute.org/igv/projects/downloads/2.18/IGV_2.18.0.zip -O tmp 
mv tmp IGV_2.18.0.zip 
unzip IGV_2.18.0.zip 
rm -f IGV_2.18.0.zip 

Set the following environment variables:

export IGV_LIB_DIRECTORY="/path/to/IGV_2.16.0/lib/"
export IGV_ARGS_FILE="path/to/igv_snapshot/igv.args"

Install Package and Dependencies

Install package with Poetry.

Install poetry:

pip install poetry
cd /path/to/igv_snapshot
poetry install

Run IGV

Example call:

python poetry \ 
igv run_screenshot \
--input-files \
"/path/to/sample.bam" \
--input-files \
"/path/to/sample.bai" \
--annotated-variant-file \
"/path/to/variant.{maf,txt,vcf}" \
-t \
"sample" \
-o \
"path/to/outdir" \
-r \
"path/to/bed/file" \
-g \
"/path/to/IGV.json"

Additional Notes

This tool by default uses the Broad hg19 reference file. See igv_snapshot/data/genome.json

If you'd like to use a different reference, you will need to download and unzip a version of IGV.

Then, you will need a JSON file specifying genome information.

And specify the JSON using the -g option.

Below is an example JSON:

{
    "id": "b37_1kg",
    "name": "Human (1kg, b37+decoy)",
    "fastaURL": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta",
    "indexURL": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai",
    "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/1kg_v37/b37_cytoband.txt",
    "aliasURL": "https://s3.amazonaws.com/igv.org.genomes/1kg_v37/b37_alias.tab",
    "tracks": [
        {
            "name": "Refseq Genes",
            "format": "refgene",
            "id": "hg19_genes",
            "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz",
            "indexed": false,
            "removable": false,
            "order": 1000000,
            "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
        }
    ],
    "chromosomeOrder": "1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17,18, 19, 20, 21, 22, X, Y"
}