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PlotInsertSizeDistributions

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,834Administrator, GATK Developer admin
edited September 2012 in GenomeSTRiP Documentation

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
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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