Display reference comparison as a tab-delimited table and summarize reference differences.
Category Reference
Overview
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.
Input
The references and MD5 calculation mode.
Output
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
Usage example
gatk CompareReferences \ -R reference1.fasta \ -refcomp reference2.fasta \ -O output.fasta \ -md5-calculation-mode USE_DICT
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by CompareReferences.
CompareReferences 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 | |
|---|---|---|---|
| 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 | |
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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--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).
The --base-comparison argument is an enumerated type (BaseComparisonMode), which can have one of the following values:
- NO_BASE_COMPARISON
- FULL_ALIGNMENT
- FIND_SNPS_ONLY
BaseComparisonMode NO_BASE_COMPARISON
--base-comparison-output
Output directory for base comparison outputs. Required for running base-comparison in FULL_ALIGNMENT or FIND_SNPS_ONLY mode.
GATKPath null
--cloud-index-prefetch-buffer / -CIPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
--create-output-variant-index / -OVI
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
boolean false
--disable-bam-index-caching / -DBIC
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
--disable-read-filter / -DF
Read filters to be disabled before analysis
List[String] []
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
--disable-tool-default-read-filters / -disable-tool-default-read-filters
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
--display-only-differing-sequences
If provided, only display sequence names that differ in their actual sequence.
boolean false
--display-sequences-by-name
If provided, the table by sequence name will be printed.
boolean false
--exclude-intervals / -XL
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] []
--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
--input / -I
BAM/SAM/CRAM file containing reads
List[GATKPath] []
--interval-exclusion-padding / -ixp
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 / -imr
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:
- ALL
- OVERLAPPING_ONLY
IntervalMergingRule ALL
--interval-padding / -ip
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 [ [ -∞ ∞ ] ]
--interval-set-rule / -isr
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:
- UNION
- Take the union of all intervals
- INTERSECTION
- Take the intersection of intervals (the subset that overlaps all intervals specified)
IntervalSetRule UNION
--intervals / -L
One or more genomic intervals over which to operate
List[String] []
--inverted-read-filter / -XRF
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
--lenient / -LE
Lenient processing of VCF files
boolean false
--max-variants-per-shard
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
--md5-calculation-mode / -md5-calculation-mode
MD5CalculationMode indicating method of MD5 calculation.
The --md5-calculation-mode argument is an enumerated type (MD5CalculationMode), which can have one of the following values:
- USE_DICT
- RECALCULATE_IF_MISSING
- ALWAYS_RECALCULATE
MD5CalculationMode RECALCULATE_IF_MISSING
--output / -O
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
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--read-filter / -RF
Read filters to be applied before analysis
List[String] []
--read-index / -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.
List[GATKPath] []
--read-validation-stringency / -VS
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:
- STRICT
- LENIENT
- SILENT
ValidationStringency SILENT
--reference / -R
Reference sequence file
R GATKPath null
--references-to-compare / -refcomp
Reference sequence file(s) to compare.
R List[GATKPath] []
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
--showHidden / -showHidden
display hidden arguments
boolean false
--sites-only-vcf-output
If true, don't emit genotype fields when writing vcf file output.
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
--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
GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.
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