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 on base quality score options
If the quality score of read bases has been modified in a previous data processing step such as GATK Base Recalibration and an OQ tag is available, this tool can be set to plot the OQ value as well as the primary quality value for the evaluation.Note: Metrics labeled as percentages are actually expressed as fractions!
Usage Example:
java -jar picard.jar QualityScoreDistribution \
I=input.bam \
O=qual_score_dist.txt \
CHART=qual_score_dist.pdf
Category Diagnostics and Quality Control
Overview
Charts quality score distribution within a BAM file.QualityScoreDistribution (Picard) 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 | |
---|---|---|---|
Required Arguments | |||
--CHART_OUTPUT -CHART |
null | A file (with .pdf extension) to write the chart to. | |
--INPUT -I |
null | Input SAM or BAM file. | |
--OUTPUT -O |
null | 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 a BAM index when writing a coordinate-sorted BAM file. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--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 |
null | 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 |
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.
--ALIGNED_READS_ONLY / NA
If set to true calculate mean quality over aligned reads only.
boolean false
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--ASSUME_SORTED / -AS
If true (default), then the sort order in the header file will be ignored.
boolean true
--CHART_OUTPUT / -CHART
A file (with .pdf extension) to write the chart to.
R File null
--COMPRESSION_LEVEL / NA
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX / NA
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
--CREATE_MD5_FILE / NA
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS / NA
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INCLUDE_NO_CALLS / NA
If set to true, include quality for no-call bases in the distribution.
boolean false
--INPUT / -I
Input SAM or BAM file.
R File null
--MAX_RECORDS_IN_RAM / NA
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 [ [ -∞ ∞ ] ]
--OUTPUT / -O
File to write the output to.
R File null
--PF_READS_ONLY / -PF
If set to true calculate mean quality over PF reads only.
boolean false
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--STOP_AFTER / NA
Stop after processing N reads, mainly for debugging.
long 0 [ [ -∞ ∞ ] ]
--TMP_DIR / NA
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY / NA
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:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY / NA
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.9.0 built at 25-11-2019 01:11:10.
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