Display reference comparison as a tab-delimited table and summarize reference differences.
This tool generates a MD5-keyed table comparing specified references and does an analysis to summarize the differences between the references provided. Comparisons are made against a "special" reference, specified with the -R argument. Subsequent references to be compared may be specified using the -references-to-compare argument. The table can be directed to a file or standard output using provided command-line arguments. A supplementary table keyed by sequence name can be displayed using the -display-sequences-by-name argument; to display only sequence names for which the references are not consistent, run with the -display-only-differing-sequences argument as well.
The references and MD5 calculation mode.
A TSV file or output stream displaying the MD5-keyed table comparison, and a table analysis displayed to standard output.
MD5 Length hg19mini.fasta hg19mini_1renamed.fasta 8c0c38e352d8f3309eabe4845456f274 16000 1 chr1 5f8388fe3fb34aa38375ae6cf5e45b89 16000 2 2 94de808a3a2203dbb02434a47bd8184f 16000 3 3 7d397ee919e379328d8f52c57a54c778 16000 4 4 REFERENCE PAIR: hg19mini.fasta, hg19mini_1renamed.fasta Status: DIFFER_IN_SEQUENCE_NAMES
gatk CompareReferences \ -R reference1.fasta \ -refcomp reference2.fasta \ -O output.fasta \ -md5-calculation-mode USE_DICT
This Read Filter is automatically applied to the data by the Engine before processing by CompareReferences.
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 | |||
| --reference -R |
Reference sequence file | ||
| --references-to-compare -refcomp |
Reference sequence file(s) to compare. | ||
| Optional Tool Arguments | |||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --base-comparison |
NO_BASE_COMPARISON | Mode for base-level comparisons. Default is off, but can do full alignment of mismatching sequences to find SNPs and INDELs (FULL_ALIGNMENT), or detect SNPs only in mismatching sequences of the same length (FIND_SNPS_ONLY). | |
| --base-comparison-output |
Output directory for base comparison outputs. Required for running base-comparison in FULL_ALIGNMENT or FIND_SNPS_ONLY mode. | ||
| --cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
| --cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
| --disable-bam-index-caching -DBIC |
false | If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. | |
| --disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
| --display-only-differing-sequences |
false | If provided, only display sequence names that differ in their actual sequence. | |
| --display-sequences-by-name |
false | If provided, the table by sequence name will be printed. | |
| --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 | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --md5-calculation-mode |
RECALCULATE_IF_MISSING | MD5CalculationMode indicating method of MD5 calculation. | |
| --output -O |
If specified, output reference sequence table in TSV format to this file. Otherwise print it to stdout. | ||
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
| --create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
| --disable-read-filter -DF |
Read filters to be disabled before analysis | ||
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
One or more genomic intervals to exclude from processing | ||
| --gatk-config-file |
A configuration file to use with the GATK. | ||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --inverted-read-filter -XRF |
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters). | ||
| --lenient -LE |
false | Lenient processing of VCF files | |
| --max-variants-per-shard |
0 | If non-zero, partitions VCF output into shards, each containing up to the given number of records. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
Read filters to be applied before analysis | ||
| --read-index |
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | ||
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
| --sequence-dictionary |
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict 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) | |
| --verbosity |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --showHidden |
false | display hidden arguments | |
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
read one or more arguments files and add them to the command line
List[File] []
Mode for base-level comparisons. Default is off, but can do full alignment of mismatching sequences to find SNPs and INDELs (FULL_ALIGNMENT), or detect SNPs only in mismatching sequences of the same length (FIND_SNPS_ONLY).
The --base-comparison argument is an enumerated type (BaseComparisonMode), which can have one of the following values:
BaseComparisonMode NO_BASE_COMPARISON
Output directory for base comparison outputs. Required for running base-comparison in FULL_ALIGNMENT or FIND_SNPS_ONLY mode.
GATKPath null
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
If provided, only display sequence names that differ in their actual sequence.
boolean false
If provided, the table by sequence name will be printed.
boolean false
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals). strings gathered from the command line -XL argument to be parsed into intervals to exclude
List[String] []
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 [ [ -∞ ∞ ] ]
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 ""
display the help message
boolean false
BAM/SAM/CRAM file containing reads
List[GATKPath] []
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
IntervalMergingRule ALL
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
Lenient processing of VCF files
boolean false
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
MD5CalculationMode indicating method of MD5 calculation.
The --md5-calculation-mode argument is an enumerated type (MD5CalculationMode), which can have one of the following values:
MD5CalculationMode RECALCULATE_IF_MISSING
If specified, output reference sequence table in TSV format to this file. Otherwise print it to stdout.
Output file will be written here. Note: If no output file provided, table will print to standard output.
GATKPath null
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value 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 --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency SILENT
Reference sequence file
R GATKPath null
Reference sequence file(s) to compare.
R List[GATKPath] []
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
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
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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.