FlagStat
A reimplementation of the 'samtools flagstat' subcommand in the GATK.
Category
Quality Control and Simple Analysis Tools
Introduction
Walks
over all input data, accumulating statistics such as total number of reads,
reads with QC failure flag set, number of duplicates, percentage mapped, etc.
FlagStat specific arguments
| Name |
Type |
Default value |
Summary |
| Required |
| --out |
PrintStream |
stdout |
An output file created by the walker. Will overwrite contents if file exists |
Additional capabilities
The arguments described in the entries below can be supplied to this tool to modify
its behavior. For example, the -L argument directs the GATK engine restricts processing
to specific genomic intervals. This capability is available to all GATK walkers.
Argument details
--out
/ -o
(
PrintStream
with default value stdout
)
An output file created by the walker. Will overwrite contents if file exists.
See also Documentation index | GATK Site | GATK support forum
GATK version 2.3-9-ge5ebf34 built at 2013/01/11 22:47:55.
