Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
PrintReads can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order. Can also optionally filter reads based on the --read_filter command line argument.
Note that when PrintReads is used as part of the Base Quality Score Recalibration workflow, it takes the --BQSR engine argument, which is listed under Inherited Arguments > CommandLineGATK below.
One or more bam files.
A single processed bam file.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T PrintReads \ -o output.bam \ -I input1.bam \ -I input2.bam \ --read_filter MappingQualityZero // Prints the first 2000 reads in the BAM file java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T PrintReads \ -o output.bam \ -I input.bam \ -n 2000 // Downsamples BAM file to 25% java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T PrintReads \ -o output.bam \ -I input.bam \ -ds 0.25
This Read Filter is automatically applied to the data by the Engine before processing by PrintReads.
This tool can be run in multi-threaded mode using this option.
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 details, see the list further down below the table.
|--downsample_coverage||double||1.0||Downsample BAM to desired coverage|
|--number||int||-1||Print the first n reads from the file, discarding the rest|
|--out||StingSAMFileWriter||stdout||Write output to this BAM filename instead of STDOUT|
|--platform||String||NA||Exclude all reads with this platform from the output|
|--readGroup||String||NA||Exclude all reads with this read group from the output|
|--sample_file||Set[File]||||File containing a list of samples (one per line). Can be specified multiple times|
|--sample_name||Set[String]||||Sample name to be included in the analysis. Can be specified multiple times.|
|--simplify||boolean||false||Simplify all reads.|
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.
Downsample BAM to desired coverage. Downsamples the bam file by the given ratio, printing only approximately the given percentage of reads. The downsampling is balanced (over the entire coverage)
Print the first n reads from the file, discarding the rest. Only prints the first n reads of the file
Write output to this BAM filename instead of STDOUT.
Exclude all reads with this platform from the output. For example, --platform ILLUMINA or --platform 454.
Exclude all reads with this read group from the output.
File containing a list of samples (one per line). Can be specified multiple times. Only reads from samples listed in the provided file(s) will be included in the output.
Sample name to be included in the analysis. Can be specified multiple times.. Only reads from the sample(s) will be included in the output.
Simplify all reads.. Erase all extra attributes in the read but keep the read group information
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.