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Single-End Statistics

se-stat

Output BAM Header including alignment statistics and parameters given any indexed (BAI) BAM File.

Command Line Interface

Usage:

java -jar ScriptManager.jar bam-statistics se-stat <bamFile>
[-hV] [-o=<output>]

Positional Input

This tool takes a single BAM file for input. As with other tools, this tool requires the BAM file be indexed.

Output Options

Option	Description
`-o, --output=<output>`	Specify output file

Command Line Interface
- Positional Input
- Output Options