A reimplementation of the 'samtools flagstat' subcommand in the GATK
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.
A BAM file containing the sequence data.
Resulting stats are written to file if an output file name is given (with -o), otherwise output to stdout.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -T FlagStat \ -R ref.fasta \ -I reads.bam \ [-o output.txt]
This Read Filter is automatically applied to the data by the Engine before processing by FlagStat.
This tool can be run in multi-threaded mode using this option.
This tool does not apply any downsampling by default.
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).
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
|Argument name(s)||Default value||Summary|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
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.
An output file created by the walker. Will overwrite contents if file exists
GATK version 3.0-0-g6bad1c6 built at 2014/03/06 06:38:04. GTD: NA