ComputeInsertSizeDistributions

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,462Administrator, GATK Developer 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

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