Write out sequence read data (for filtering, merging, subsetting etc)
PrintReads is a generic utility tool for manipulating sequencing data in SAM/BAM format. It can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order. It can also optionally filter reads based on various read properties such as read group tags using the `--read_filter/-rf` command line argument (see documentation on read filters for more information).
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.
// Prints all reads that have a mapping quality above zero java -jar GenomeAnalysisTK.jar \ -T PrintReads \ -R reference.fasta \ -I input1.bam \ -I input2.bam \ -o output.bam \ --read_filter MappingQualityZero // Prints the first 2000 reads in the BAM file java -jar GenomeAnalysisTK.jar \ -T PrintReads \ -R reference.fasta \ -I input.bam \ -o output.bam \ -n 2000 // Downsamples BAM file to 25% java -jar GenomeAnalysisTK.jar \ -T PrintReads \ -R reference.fasta \ -I input.bam \ -o output.bam \ -dfrac 0.25
These Read Filters are automatically applied to the data by the Engine before processing by PrintReads.
This tool can be run in multi-threaded mode using this option.
This tool does not apply any downsampling by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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 | |
|---|---|---|---|
| Optional Outputs | |||
| --out -o |
stdout | Write output to this BAM filename instead of STDOUT | |
| Optional Parameters | |||
| --number -n |
-1 | Print the first n reads from the file, discarding the rest | |
| --platform |
NA | Exclude all reads with this platform from the output | |
| --readGroup |
NA | Exclude all reads with this read group from the output | |
| --sample_file -sf |
[] | File containing a list of samples (one per line). Can be specified multiple times | |
| --sample_name -sn |
[] | Sample name to be included in the analysis. Can be specified multiple times. | |
| Optional Flags | |||
| --simplify -s |
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.
Print the first n reads from the file, discarding the rest
Only prints the first n reads of the file
int -1 [ [ -∞ ∞ ] ]
Write output to this BAM filename instead of STDOUT
GATKSAMFileWriter stdout
Exclude all reads with this platform from the output
For example, --platform ILLUMINA or --platform 454.
String NA
Exclude all reads with this read group from the output
String NA
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.
Set[File] []
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.
Set[String] []
Simplify all reads
Erase all extra attributes in the read but keep the read group information
boolean false