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CompareBaseQualities

Compares the base qualities of two SAM/BAM/CRAM files

Category Diagnostics and Quality Control


Overview

Compares the base qualities of two SAM/BAM/CRAM files. The reads in the two files must have exactly the same names and appear in the same order. The two files are each specified without a flag. The tool summarizes the results in a text file.

Usage example

 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
 

CompareBaseQualities 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
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
--gcs-project-for-requester-pays
"" Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--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
null Temp directory to use.
--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)

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.


[NA - Positional] / NA

Undocumented option
Undocumented option

R List[File]  NA


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and GELI).

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


--gatk-config-file / NA

A configuration file to use with the GATK.

String  null


--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]


--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""


--help / -h

display the help message

boolean  false


--MAX_RECORDS_IN_RAM / NA

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  [ [ -∞  ∞ ] ]


--output / -O

Summary output file.

String  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--reference / -R

Reference sequence file.

File  null


--round-down-quantized / NA

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


--showHidden / -showHidden

display hidden arguments

boolean  false


--static-quantized-quals / NA

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-on-diff / NA

Throw exception on difference.

boolean  false


--tmp-dir / NA

Temp directory to use.

String  null


--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false


--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

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 / -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 / NA

display the version number for this tool

boolean  false


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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.