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 \
   -dfrac 0.25
 

Additional Information

Read filters

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

Parallelism options

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

Downsampling settings

This tool does not apply any downsampling by default.


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).

PrintReads specific arguments

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.

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.


--number / -n

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

int  -1  [ [ -?  ? ] ]


--out / -o

Write output to this BAM filename instead of STDOUT

GATKSAMFileWriter  stdout


--platform / -platform

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

String


--readGroup / -readGroup

Exclude all reads with this read group from the output

String


--sample_file / -sf

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 / -sn

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 / -s

Simplify all reads.
Erase all extra attributes in the read but keep the read group information

boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA