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1. Introduction

The MergeGenotyperOutput utility merges the results of a parallel genotyping 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.

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