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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
-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).
-O <histogram-file>: Location of the output binary histogram file.
Geraldine Van der Auwera, PhD