PlotInsertSizeDistributions

Geraldine_VdAuwera

1. Introduction

The PlotInsertSizeDistributions generates plots of the insert size distributions of each sequencing library.

For sequencing libraries with paired reads, one can measure the empirical distribution of the lengths of the DNA fragments in the library. Genome STRiP measures and models these insert size distributions and uses the modeled distributions for discovery and for genotyping. This utility plots the insert size distributions as modeled by Genome STRiP.

2. Inputs / Arguments

• -I <histogram-file> : The input binary histogram file containing the insert size distribution data [required]. : Currently only isd.hist.bin files are supported (not the reduced representation isd.dist.bin files).

• -library <library-ID> : The library or libraries to plot (this argument may be specified multiple times or as a .list file with extension .list containing one library ID per line).

• -sample <sample-ID> : The sample or samples to plot (this argument may be specified multiple times or as a .list file with extension .list containing one sample ID per line).

3. Outputs

• -O <output-file> : The destination output file (PDF) [required].

4. Running

java -Xmx2g -cp SVToolkit.jar:GenomeAnalysisTK.jar \
    org.broadinstitute.sv.apps.PlotInsertSizeDistributions \ 
    -I metadata/isd.hist.bin \ 
    -sample NA12878 \ 
    -O my_output_file.pdf