Collect metrics about reads that pass quality thresholds and Illumina-specific filters. This tool evaluates the overall quality of reads within a bam file containing one read group. The output indicates the total numbers of bases within a read group that pass a minimum base quality score threshold and (in the case of Illumina data) pass Illumina quality filters as described in the GATK Dictionary entry.
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 use the OQ value instead of the primary quality value for the evaluation.Note that the default behaviour of this program changed as of November 6th 2015 to no longer include secondary and supplemental alignments in the computation.
Usage Example:
java -jar picard.jar CollectQualityYieldMetrics \Please see the QualityYieldMetrics documentation for details and explanations of the output metrics.
I=input.bam \
O=quality_yield_metrics.txt \
Category Diagnostics and Quality Control
Overview
Command line program to calibrate quality yield metricsCollectQualityYieldMetrics (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 | |||
--INPUT -I |
null | Input SAM or BAM file. | |
--OUTPUT -O |
null | File to write the output to. | |
Optional Tool Arguments | |||
--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_SECONDARY_ALIGNMENTS |
false | If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file. | |
--INCLUDE_SUPPLEMENTAL_ALIGNMENTS |
false | If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file. | |
--STOP_AFTER |
0 | Stop after processing N reads, mainly for debugging. | |
--USE_ORIGINAL_QUALITIES -OQ |
true | If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field. | |
--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.
--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
--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_SECONDARY_ALIGNMENTS / NA
If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file.
boolean false
--INCLUDE_SUPPLEMENTAL_ALIGNMENTS / NA
If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file.
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
--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
--USE_ORIGINAL_QUALITIES / -OQ
If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field.
boolean true
--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 4.0.1.2 built at 02-02-2019 02:02:55.
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