Compares the base qualities of two SAM/BAM/CRAM files
gatk CompareBaseQualities \ input_1.bam \ input_2.bam \ -O diff.txt
An example result with identical base qualities between two inputs
-----------CompareMatrix summary------------ all 10000 quality scores are the same ---------CompareMatrix full matrix (non-zero entries) ---------- QRead1 QRead2 diff count 40 40 0 10000 -----------CompareMatrix-binned summary------------ all 10000 quality scores are the same ---------CompareMatrix-binned full matrix (non-zero entries) ---------- QRead1 QRead2 diff count 40 40 0 10000
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 | |
|---|---|---|---|
| Positional Arguments | |||
| [NA - Positional] |
NA | Undocumented option | |
| Optional Tool Arguments | |||
| --arguments_file |
[] | read one or more arguments files and add them to the command line | |
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --help -h |
false | display the help message | |
| --output -O |
null | Summary output file. | |
| --throw-on-diff |
false | Throw exception on difference. | |
| --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 GELI). | |
| --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. | |
| --gatk-config-file |
null | A configuration file to use with the GATK. | |
| --MAX_RECORDS_IN_RAM |
500000 | When writing SAM 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 a SAM file, and increases the amount of RAM needed. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --reference -R |
null | Reference sequence file. | |
| --TMP_DIR |
[] | Undocumented option | |
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --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 | |||
| --round-down-quantized |
false | Round down quality scores to nearest quantized value. | |
| --showHidden |
false | display hidden arguments | |
| --static-quantized-quals |
[] | Use static quantized quality scores to a given number of levels (with --bqsr-recal-file) | |
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.
Undocumented option
Undocumented option
R List[File] NA
read one or more arguments files and add them to the command line
List[File] []
Compression level for all compressed files created (e.g. BAM and GELI).
int 5 [ [ -∞ ∞ ] ]
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
display the help message
boolean false
When writing SAM 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 a SAM file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
Summary output file.
String null
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
File null
Round down quality scores to nearest quantized value.
Round down quantized only works with the {@link #STATIC_QUANTIZED_QUALS_LONG_NAME} option. If enabled,
rounding is done in probability space to the nearest bin. Otherwise, the value is rounded to the
nearest bin that is smaller than the current bin.
Note: this option only works when {@link #STATIC_QUANTIZED_QUALS_LONG_NAME} is set.
boolean false
display hidden arguments
boolean false
Use static quantized quality scores to a given number of levels (with --bqsr-recal-file)
Return value is 0 if the two files have identical base qualities and non-zero otherwise.
Use static quantized quality scores to a given number of levels.
List[Integer] []
Throw exception on difference.
boolean false
Undocumented option
List[File] []
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
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 Docs Index | Support Forum
GATK version 4.0.3.0 built at 09-43-2018 09:43:10.