FlagStat

A reimplementation of the 'samtools flagstat' subcommand in the GATK

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ

Overview

This tool 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.

Input

A BAM file containing the sequence data.

Output

Resulting stats are written to file if an output file name is given (with -o), otherwise output to stdout.

Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -T FlagStat \
   -R ref.fasta \
   -I reads.bam \
   [-o output.txt]

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by FlagStat.

MalformedReadFilter

Parallelism options

This tool can be run in multi-threaded mode using this option.

NanoSchedulable (-nct)

Command-line Arguments

Inherited arguments

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 is an Engine capability and is therefore available to all GATK walkers).

CommandLineGATK

FlagStat specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--out / -o ( PrintStream with default value stdout )

An output file created by the walker. Will overwrite contents if file exists.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.