Collect statistics about read groups and their properties
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.
Any number of BAM files
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
java -jar GenomeAnalysisTK.jar \
-T ReadGroupProperties \
-R reference.fasta \
-I example1.bam \
-I example2.bam \
-o readgroup_report.grp
These Read Filters are automatically applied to the data by the Engine before processing by ReadGroupProperties.
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 | 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 | |
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.
Calculate median from the first maxElementsForMedian values observed
int 10000 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout