IGV Batch Generator

Given an input of a CSV file containing gene loci and a mapping of samples to their corresponding BAM files, creates an IGV batch script that will save images of the corresponding genetic loci.

The generated file must be run by IGV in order to generate the specified images.

Input Data

This script expects the following headers in the input CSV file. There currently is no support for .xls or .xlsx files.

SampleID
CHROM
POS

Installation

Change the SAMPLE_BAM_MAPPING_LOCATION variable in batch_generator.py to reflect the location of the sample map file. Alternatively, supply the -m flag when running batch_generator.py.

Running batch_generator on Orchestra

On Orchestra, execute the following command at the command prompt (omit the $, which is a customary indicator of the command prompt line):

$ /opt/java/jdk1.8.0_45/bin/java -Xmx3000m -jar /opt/IGV_2.3.57/igv.jar -b BATCH_FILE_PATH

• NB: Certain commands may fail when the batch file is run directly from the command-line, notably maxPanelHeight and expand