PrintReads

Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ

Overview

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.

Input

One or more bam files.

Output

A single processed bam file.

Examples

 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

Additional Information

Read filters

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

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

PrintReads 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
--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.

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.

--downsample_coverage / -ds ( double with default value 1.0 )

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)

--number / -n ( int with default value -1 )

Print the first n reads from the file, discarding the rest. Only prints the first n reads of the file

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

Write output to this BAM filename instead of STDOUT.

--platform / -platform ( String )

Exclude all reads with this platform from the output. For example, --platform ILLUMINA or --platform 454.

--readGroup / -readGroup ( String )

Exclude all reads with this read group from the output.

--sample_file / -sf ( Set[File] with default value [] )

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 / -sn ( Set[String] with default value [] )

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 / -s ( boolean with default value false )

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.