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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
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# MergeDiscoveryOutput

edited September 2012

### 1. Introduction

The MergeDiscoveryOutput utility merges the results of a parallel discovery
run into genome-wide output files.

In addition to merging the main VCF files, this utility will also merge the
auxilliary output files (but leave them in the run directory).

### 2. Inputs / Arguments

• -runDirectory <directory> : The run directory where the output files from
each partition are stored.

### 3. Outputs

• -O <vcf-file>` : The location to write the merged output VCF file.
Post edited by Geraldine_VdAuwera on
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