The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at


Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,985 admin
edited September 2012 in GenomeSTRiP Documentation

1. Introduction

The ComputeInsertSizeDistributions walker traverses a set of BAM files to generate histograms of insert sizes.

The insert size histograms are stored in a binary file format. Many histograms can be stored in the same file. The histograms are identified by <Sample, Library, ReadGroup> triples. The trailing components can be null. For example,
if histograms are computed library-by-library (the default), then the ReadGroup in each triple will be null.

See also MergeInsertSizeDistributions, ComputeInsertStatistics.

2. Inputs / Arguments

  • -I <bam-file> : The set of input BAM files.

  • -md <directory> : The metadata directory. Currently only used to check for a default list of excluded read groups.

  • -overwrite : If true (the default), overwrite the output file, otherwise append.

  • -createEmpty : If true, create a zero length output file if there are no paired reads in the input (default false).

3. Outputs

  • -O <histogram-file> : Location of the output binary histogram file.
Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Sign In or Register to comment.