Collect mean quality by cycle.This tool generates a data table and chart of mean quality by cycle from a BAM file. It is intended to be used on a single lane or a read group's worth of data, but can be applied to merged BAMs if needed.
This metric gives an overall snapshot of sequencing machine performance. For most types of sequencing data, the output is expected to show a slight reduction in overall base quality scores towards the end of each read. Spikes in quality within reads are not expected and may indicate that technical problems occurred during sequencing.
Note: Metrics labeled as percentages are actually expressed as fractions!
Usage example:
java -jar picard.jar MeanQualityByCycle \
I=input.bam \
O=mean_qual_by_cycle.txt \
CHART=mean_qual_by_cycle.pdf
Category Diagnostics and Quality Control
Overview
Program to generate a data table and chart of mean quality by cycle from a BAM file. Works best on a single lane/run of data, but can be applied to merged BAMs - the output may just be a little confusing.MeanQualityByCycle (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 |
A file (with .pdf extension) to write the chart to. | ||
--INPUT -I |
Input SAM or BAM 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 | |
--PF_READS_ONLY |
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 |
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
If set to true, calculate mean quality over aligned reads only.
boolean false
--arguments_file
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
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INPUT / -I
Input SAM or BAM file.
R File null
--MAX_RECORDS_IN_RAM
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
The file to write the output to.
R File null
--PF_READS_ONLY
If set to true calculate mean quality over PF reads only.
boolean false
--QUIET
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
Stop after processing N reads, mainly for debugging.
long 0 [ [ -∞ ∞ ] ]
--TMP_DIR
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
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
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
display the version number for this tool
boolean false
GATK version 4.1.8.0-SNAPSHOT built at Tue, 30 Jun 2020 17:28:31 -0400.
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