Showing docs for version 3.6-0 | The latest version is 4.1.4.0


ReadGroupProperties

Collect statistics about read groups and their properties

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


Overview

This tool emits a GATKReport containing read group, sample, library, platform, center, sequencing data, paired end status, simple read type name (e.g. 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 on whole genome sequence data and expect it to finish in an appropriate timeframe.

Input

Any number of BAM files

Output

GATKReport containing read group, sample, library, platform, center, median insert size and median read length. For example, running this tool on the NA12878 data sets:

      ##:GATKReport.v0.2 ReadGroupProperties : Table of read group properties
      readgroup  sample   library       platform  center  date     has.any.reads  is.paired.end  n.reads.analyzed  simple.read.type  median.read.length  median.insert.size
      20FUK.1    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        498  2x101                            101                 386
      20FUK.2    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        476  2x101                            101                 417
      20FUK.3    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        407  2x101                            101                 387
      20FUK.4    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        389  2x101                            101                 415
      20FUK.5    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        433  2x101                            101                 386
      20FUK.6    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        480  2x101                            101                 418
      20FUK.7    NA12878  Solexa-18483  illumina  BI      2/2/10   true           true                        450  2x101                            101                 386
      20FUK.8    NA12878  Solexa-18484  illumina  BI      2/2/10   true           true                        438  2x101                            101                 418
      20GAV.1    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        490  2x101                            101                 391
      20GAV.2    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        485  2x101                            101                 417
      20GAV.3    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        460  2x101                            101                 392
      20GAV.4    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        434  2x101                            101                 415
      20GAV.5    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        479  2x101                            101                 389
      20GAV.6    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        461  2x101                            101                 416
      20GAV.7    NA12878  Solexa-18483  illumina  BI      1/26/10  true           true                        509  2x101                            101                 386
      20GAV.8    NA12878  Solexa-18484  illumina  BI      1/26/10  true           true                        476  2x101                            101                 410                           101                 414
      

Usage example

    java -jar GenomeAnalysisTK.jar \
      -T ReadGroupProperties \
      -R reference.fasta \
      -I example1.bam \
      -I example2.bam \
      -o readgroup_report.grp
  

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by ReadGroupProperties.

Downsampling settings

This tool does not apply any downsampling by default.


Command-line Arguments

Engine arguments

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.

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

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

Calculate median from the first maxElementsForMedian values observed

int  10000  [ [ -∞  ∞ ] ]


--out / -o

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

PrintStream  stdout


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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.