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. User must have storage.buckets.get permission on the bucket being accessed.
--help -h	false	display the help message
--output -O		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		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		Reference sequence file.
--tmp-dir		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]

Undocumented option
Undocumented option

R List[GATKPath] NA

--arguments_file

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

List[File] []

--COMPRESSION_LEVEL

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

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

--gatk-config-file

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

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String ""

--help / -h

display the help message

boolean false

--MAX_RECORDS_IN_RAM

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

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

Boolean false

--reference / -R

Reference sequence file.

File null

--round-down-quantized

Round down quality scores to nearest quantized value.
Round down quantized only works with the 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 is set.

boolean false

--showHidden / -showHidden

display hidden arguments

boolean false

--static-quantized-quals

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

Throw exception on difference.

boolean false

--tmp-dir

Temp directory to use.

GATKPath 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

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

display the version number for this tool

boolean false

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.