ReadGroupProperties

Emits a GATKReport containing read group, sample, library, platform, center, sequencing data, paired end status, simple read type name (e.g.

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ

Overview

2x76) median insert size and median read length for each read group in every provided BAM file Note that this walker stops when all read groups have been observed at least a few thousand times so that the median statistics are well determined. It is safe to run it WG and it'll finish in an appropriate timeframe.

Input

Any number of BAM files

Output

GATKReport containing read group, sample, For example, running this tool on the

 ##:GATKReport.v0.2 ReadGroupProperties readgroup  sample   library       platform  center  date 20FUK.1    NA12878  Solexa-18483  illumina  BI 20FUK.2    NA12878  Solexa-18484  illumina  BI 20FUK.3    NA12878  Solexa-18483  illumina  BI 20FUK.4    NA12878  Solexa-18484  illumina  BI 20FUK.5    NA12878  Solexa-18483  illumina  BI 20FUK.6    NA12878  Solexa-18484  illumina  BI 20FUK.7    NA12878  Solexa-18483  illumina  BI 20FUK.8    NA12878  Solexa-18484  illumina  BI 20GAV.1    NA12878  Solexa-18483  illumina  BI 20GAV.2    NA12878  Solexa-18484  illumina  BI 20GAV.3    NA12878  Solexa-18483  illumina  BI 20GAV.4    NA12878  Solexa-18484  illumina  BI 20GAV.5    NA12878  Solexa-18483  illumina  BI 20GAV.6    NA12878  Solexa-18484  illumina  BI 20GAV.7    NA12878  Solexa-18483  illumina  BI 20GAV.8    NA12878  Solexa-18484  illumina  BI

library, platform, center, median insert size and median read length. NA12878 data sets: : Table of read group properties has.any.reads is.paired.end n.reads.analyzed simple.read.type median.read.length median.insert.size 2/2/10 true true 498 2x101 101 386 2/2/10 true true 476 2x101 101 417 2/2/10 true true 407 2x101 101 387 2/2/10 true true 389 2x101 101 415 2/2/10 true true 433 2x101 101 386 2/2/10 true true 480 2x101 101 418 2/2/10 true true 450 2x101 101 386 2/2/10 true true 438 2x101 101 418 1/26/10 true true 490 2x101 101 391 1/26/10 true true 485 2x101 101 417 1/26/10 true true 460 2x101 101 392 1/26/10 true true 434 2x101 101 415 1/26/10 true true 479 2x101 101 389 1/26/10 true true 461 2x101 101 416 1/26/10 true true 509 2x101 101 386 1/26/10 true true 476 2x101 101 410 101 414

Examples

    java
      -jar GenomeAnalysisTK.jar
      -T ReadGroupProperties
      -I example1.bam -I example2.bam etc
      -R reference.fasta
      -o example.gatkreport.txt

Additional Information

Read filters

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

MalformedReadFilter

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

ReadGroupProperties 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
--max_values_for_median	int	10000	Calculate median from the first maxElementsForMedian values observed
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

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.

--max_values_for_median / -maxElementsForMedian ( int with default value 10000 )

Calculate median from the first maxElementsForMedian values observed.

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

An output file created by the walker. Will overwrite contents if file exists.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.