Chart the distribution of quality scores.
This tool is used for determining the overall 'quality' for a library in a given run. To that effect, it outputs a chart and tables indicating the range of quality scores and the total numbers of bases corresponding to those scores. Options include plotting the distribution of all of the reads, only the aligned reads, or reads that have passed the Illumina Chastity filter thresholds as described here.
Note: Metrics labeled as percentages are actually expressed as fractions!
java -jar picard.jar QualityScoreDistribution \
I=input.bam \
O=qual_score_dist.txt \
CHART=qual_score_dist.pdf
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 | |
|---|---|---|---|
| Required Arguments | |||
| --CHART_OUTPUT -CHART |
A file (with .pdf extension) to write the chart to. | ||
| --INPUT -I |
Input SAM/BAM/CRAM file. | ||
| --OUTPUT -O |
The file to write the output to. | ||
| Optional Tool Arguments | |||
| --ALIGNED_READS_ONLY |
false | If set to true calculate mean quality over aligned reads only. | |
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --ASSUME_SORTED -AS |
true | If true (default), then the sort order in the header file will be ignored. | |
| --help -h |
false | display the help message | |
| --INCLUDE_NO_CALLS |
false | If set to true, include quality for no-call bases in the distribution. | |
| --PF_READS_ONLY -PF |
false | If set to true calculate mean quality over PF reads only. | |
| --STOP_AFTER |
0 | Stop after processing N reads, mainly for debugging. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
| --CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
| --CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
| --MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
| --TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
| --USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
| --USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
| --VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --VERBOSITY |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --showHidden |
false | display hidden arguments | |
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.
If set to true calculate mean quality over aligned reads only.
boolean false
read one or more arguments files and add them to the command line
List[File] []
If true (default), then the sort order in the header file will be ignored.
boolean true
A file (with .pdf extension) to write the chart to.
R File null
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
display the help message
boolean false
If set to true, include quality for no-call bases in the distribution.
boolean false
Input SAM/BAM/CRAM file.
R File null
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
The file to write the output to.
R File null
If set to true calculate mean quality over PF reads only.
boolean false
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
PicardHtsPath null
display hidden arguments
boolean false
Stop after processing N reads, mainly for debugging.
long 0 [ [ -∞ ∞ ] ]
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency STRICT
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.