Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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
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).
-O <histogram-file>: Location of the output binary histogram file.