vcfigv

vcfigv allows the automated production of an IGV batch file from a VCF of SNPs and small indels, which enables the creation of screenshots surrounding each of the variants in the file.

Compilation

javac src/*.java

Running

Usage: java -cp src Vcf2Bat [args]
  Example: java -cp src Vcf2Bat aln=jhu004.bam var=snps.vcf genome=ref.fasta

Required args:
  aln    (String) - a BAM file with the read alignments
  var    (String) - a VCF file with the variants to visualize
  genome (String) - a FASTA file with the reference genome

Optional args:
  padding      (int)    [50]     - the number of bases on each side of the variant to include
  outprefix (String)    [igv]    - the name of the directory to put screenshots into
  --nocombine                    - don't combine nearby variants into single screenshots
  --squish                       - squish the screenshots to capture more reads
  --svg                          - output the snapshots to svg files instead of png files

Then, in IGV (v1.5+), click on Tools->Run Batch Script, and select the generated batch script igv.bat from the working directory.

Generating screenshots from the command line

To run the batch script from the command line instead of the IGV interface, an off-screen server such as xvfb is required. The following commands show how to do this:

sudo apt-get install xvfb
xvfb-run --auto-servernum PATH_TO/igv.sh -b BATCH_FILE