CompareSAMs (Picard)

Compare two input SAM/BAM/CRAM files. This tool initially compares the headers of the input files. If the file headers are comparable, the tool can perform either strict comparisons for which each alignment and the header must be identical, or a more lenient check of "equivalence", where reads with mapping quality < LOW_MQ_THRESHOLD are allowed to have different alignments, duplicate marks are allowed to differ to account for ambiguities in selecting the representative read of a duplicate set, and some differences in headers is allowed. By default, alignment comparisons, duplicate marking comparisons, and header comparisons are performed in the strict mode. Results of comparison are summarised in an output metrics file.

Usage example:

CompareSAMs for exact matching:

java -jar picard.jar CompareSAMs \
      file_1.bam \
      file_2.bam \
      O=comparison.tsv

CompareSAMs for "equivalence":

java -jar picard.jar CompareSAMs \
file_1.bam \
file_2.bam \
LENIENT_LOW_MQ_ALIGNMENT=true \
LENIENT_DUP=true \
O=comparison.tsv

CompareSAMs for "equivalence", allow certain differences in header:

java -jar picard.jar CompareSAMs \
file_1.bam \
file_2.bam \
LENIENT_LOW_MQ_ALIGNMENT=true \
LENIENT_DUP=true \
LENIENT_HEADER=true \
O=comparison.tsv

Category Diagnostics and Quality Control

Overview

Rudimentary SAM comparer. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info. Summarizes the number of alignments that match, mismatch, are missing, etc. @author alecw@broadinstitute.org

CompareSAMs (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
Positional Arguments
[NA - Positional]	NA	Exactly two input SAM/BAM/CRAM files to compare to one another.
Optional Tool Arguments
--arguments_file		read one or more arguments files and add them to the command line
--COMPARE_MQ	false	If set to true, generate a histogram for mapping quality concordance between the two SAM files and write it to the output metrics file. In this histogram, an entry of 10 at bin "20,30" means that 10 reads in the left file have mapping quality 20 while those same reads have mapping quality 30 in the right file. The reads are associated based solely on read names and not the mapped position. Only primary alignments are included, but all duplicate reads are counted individually.
--help -h	false	display the help message
--LENIENT_DUP	false	Perform lenient checking of duplicate marks. In this mode, will reduce the number of mismatches by allowing the choice of the representative read in each duplicate set to differ between the input files, as long as the duplicate sets agree.
--LENIENT_HEADER	false	Perform lenient checking of header. In this mode, species, assembly, ur, m5, fields of sequence records, and pg fields in the header may all differ. Sequence record length must also be the same.
--LENIENT_LOW_MQ_ALIGNMENT	false	Count reads which have mapping quality below LOW_MQ_THRESHOLD in both files but are mapped to different locations as matches. By default we count such reads as mismatching.
--LENIENT_UNKNOWN_MQ_ALIGNMENT	false	Count reads for which no mapping quality is available (mapping quality value 255) in both files but are mapped to different locations as matches. By default we count such reads as mismatching.
--LOW_MQ_THRESHOLD	3	When running in LENIENT_LOW_MQ_ALIGNMENT mode, reads which have mapping quality below this value will be counted as matches. if LENIENT_LOW_MQ_ALIGNMENT is false (default), then this argument has no effect.
--OUTPUT -O		Output file to write comparison results to.
--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 an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	false	Whether to create an MD5 digest for any BAM or FASTQ files created.
--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.

[NA - Positional]

Exactly two input SAM/BAM/CRAM files to compare to one another.
Exactly two input SAM/BAM/CRAM files to compare to one another.

R List[File] NA

--arguments_file

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

List[File] []

--COMPARE_MQ

If set to true, generate a histogram for mapping quality concordance between the two SAM files and write it to the output metrics file. In this histogram, an entry of 10 at bin "20,30" means that 10 reads in the left file have mapping quality 20 while those same reads have mapping quality 30 in the right file. The reads are associated based solely on read names and not the mapped position. Only primary alignments are included, but all duplicate reads are counted individually.

boolean false

--COMPRESSION_LEVEL

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

int 5 [ [ -∞ ∞ ] ]

--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean false

--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean false

--help / -h

display the help message

boolean false

--LENIENT_DUP

Perform lenient checking of duplicate marks. In this mode, will reduce the number of mismatches by allowing the choice of the representative read in each duplicate set to differ between the input files, as long as the duplicate sets agree.

boolean false

--LENIENT_HEADER

Perform lenient checking of header. In this mode, species, assembly, ur, m5, fields of sequence records, and pg fields in the header may all differ. Sequence record length must also be the same.

boolean false

--LENIENT_LOW_MQ_ALIGNMENT

Count reads which have mapping quality below LOW_MQ_THRESHOLD in both files but are mapped to different locations as matches. By default we count such reads as mismatching.

boolean false

--LENIENT_UNKNOWN_MQ_ALIGNMENT

Count reads for which no mapping quality is available (mapping quality value 255) in both files but are mapped to different locations as matches. By default we count such reads as mismatching.

boolean false

--LOW_MQ_THRESHOLD

When running in LENIENT_LOW_MQ_ALIGNMENT mode, reads which have mapping quality below this value will be counted as matches. if LENIENT_LOW_MQ_ALIGNMENT is false (default), then this argument has no effect.

int 3 [ [ -∞ ∞ ] ]

--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

Output file to write comparison results to.

File null

--QUIET

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath null

--showHidden / -showHidden

display hidden arguments

boolean false

--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

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