MarkDuplicates on Spark
Category Read Data Manipulation
Overview
This is a Spark implementation of the MarkDuplicates tool from Picard that allows the tool to be run in parallel on multiple cores on a local machine or multiple machines on a Spark cluster while still matching the output of the single-core Picard version. Since the tool requires holding all of the readnames in memory while it groups the read information, it is recommended running this tool on a machine/configuration with at least 8 GB of memory overall for a typical 30x bam.
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library construction using PCR. See also "EstimateLibraryComplexity" + for additional notes on PCR duplication artifacts. Duplicate reads can also result from a single amplification cluster, incorrectly detected as multiple clusters by the optical sensor of the sequencing instrument. These duplication artifacts are referred to as optical duplicates.
The MarkDuplicates tool works by comparing sequences in the 5 prime positions of both reads and read-pairs in a SAM/BAM file. After duplicate reads are collected, the tool differentiates the primary and duplicate reads using an algorithm that ranks reads by the sums of their base-quality scores (default method).
The tool's main output is a new SAM or BAM file, in which duplicates have been identified in the SAM flags field for each read. Duplicates are marked with the hexadecimal value of 0x0400, which corresponds to a decimal value of 1024. If you are not familiar with this type of annotation, please see the following blog post for additional information.
" +Although the bitwise flag annotation indicates whether a read was marked as a duplicate, it does not identify the type of duplicate. To do this, a new tag called the duplicate type (DT) tag was recently added as an optional output in the 'optional field' section of a SAM/BAM file. Invoking the 'duplicate-tagging-policy' option, you can instruct the program to mark all the duplicates (All), only the optical duplicates (OpticalOnly), or no duplicates (DontTag). The records within the output of a SAM/BAM file will have values for the 'DT' tag (depending on the invoked 'duplicate-tagging-policy'), as either library/PCR-generated duplicates (LB), or sequencing-platform artifact duplicates (SQ). This tool uses the 'read-name-regex' and the 'optical-duplicate-pixel-distance' options as the primary methods to identify and differentiate duplicate types. Set read-name-regex' to null to skip optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate.
MarkDuplicates also produces a metrics file indicating the numbers of duplicates for both single- and paired-end reads.
The program can take either coordinate-sorted or query-sorted inputs, however it is recommended that the input be query-sorted or query-grouped as the tool will have to perform an extra sort operation on the data in order to associate reads from the input bam with their mates.
If desired, duplicates can be removed using the 'remove-all-duplicates' and 'remove-sequencing-duplicates' options.
Usage example:
gatk MarkDuplicatesSpark \\
-I input.bam \\
-O marked_duplicates.bam \\
-M marked_dup_metrics.txt
MarkDuplicates run locally specifying the core input (if 'spark.executor.cores' is unset spark will use all available cores on the machine)
gatk MarkDuplicatesSpark \\
-I input.bam \\
-O marked_duplicates.bam \\
-M marked_dup_metrics.txt \\
--conf 'spark.executor.cores=5'
MarkDuplicates run on a spark cluster 5 machines
gatk MarkDuplicatesSpark \\Please see MarkDuplicates for detailed explanations of the output metrics.
-I input.bam \\
-O marked_duplicates.bam \\
-M marked_dup_metrics.txt \\
-- \\
--spark-runner SPARK \\
--spark-master \\
--num-executors 5 \\
--executor-cores 8
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by MarkDuplicatesSpark.
MarkDuplicatesSpark 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 | |||
--input -I |
[] | BAM/SAM/CRAM file containing reads | |
--output -O |
null | the output bam | |
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--bam-partition-size |
0 | maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block). | |
--conf |
[] | spark properties to set on the spark context in the format = | |
--disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
--do-not-mark-unmapped-mates |
false | Enabling this option will mean unmapped mates of duplicate marked reads will not be marked as duplicates. | |
--duplicate-scoring-strategy -DS |
SUM_OF_BASE_QUALITIES | The scoring strategy for choosing the non-duplicate among candidates. | |
--duplicate-tagging-policy |
DontTag | Determines how duplicate types are recorded in the DT optional attribute. | |
--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 | |
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
[] | One or more genomic intervals over which to operate | |
--metrics-file -M |
null | Path to write duplication metrics to. | |
--num-reducers |
0 | For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input. | |
--optical-duplicate-pixel-distance |
100 | The maximum offset between two duplicate clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. | |
--output-shard-tmp-dir |
null | when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used | |
--program-name |
null | Name of the program running | |
--read-name-regex |
Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values. | ||
--reference -R |
null | Reference sequence | |
--remove-all-duplicates |
false | If true do not write duplicates to the output file instead of writing them with appropriate flags set. | |
--remove-sequencing-duplicates |
false | If true do not write optical/sequencing duplicates to the output file instead of writing them with appropriate flags set. | |
--sharded-output |
false | For tools that write an output, write the output in multiple pieces (shards) | |
--spark-master |
local[*] | URL of the Spark Master to submit jobs to when using the Spark pipeline runner. | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--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 index when writing a coordinate-sorted BAM file. | |
--create-output-bam-splitting-index |
true | If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file. | |
--create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
--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 |
null | A configuration file to use with the GATK. | |
--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 | |
--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. | |
--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) | |
--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-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--bam-partition-size / NA
maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).
long 0 [ [ -∞ ∞ ] ]
--conf / -conf
spark properties to set on the spark context in the format =
List[String] []
--create-output-bam-index / -OBI
If true, create a BAM index when writing a coordinate-sorted BAM file.
boolean true
--create-output-bam-splitting-index / NA
If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
boolean true
--create-output-variant-index / -OVI
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
--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
--do-not-mark-unmapped-mates / NA
Enabling this option will mean unmapped mates of duplicate marked reads will not be marked as duplicates.
boolean false
--duplicate-scoring-strategy / -DS
The scoring strategy for choosing the non-duplicate among candidates.
The --duplicate-scoring-strategy argument is an enumerated type (MarkDuplicatesScoringStrategy), which can have one of the following values:
- SUM_OF_BASE_QUALITIES
- TOTAL_MAPPED_REFERENCE_LENGTH
MarkDuplicatesScoringStrategy SUM_OF_BASE_QUALITIES
--duplicate-tagging-policy / NA
Determines how duplicate types are recorded in the DT optional attribute.
Exclusion: This argument cannot be used at the same time as remove-all-duplicates, remove-sequencing-duplicates
.
The --duplicate-tagging-policy argument is an enumerated type (DuplicateTaggingPolicy), which can have one of the following values:
- DontTag
- OpticalOnly
- All
DuplicateTaggingPolicy DontTag
--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).
List[String] []
--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
--input / -I
BAM/SAM/CRAM file containing reads
R List[String] []
--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] []
--metrics-file / -M
Path to write duplication metrics to.
String null
--num-reducers / NA
For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.
int 0 [ [ -∞ ∞ ] ]
--optical-duplicate-pixel-distance / NA
The maximum offset between two duplicate clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal.
int 100 [ [ -∞ ∞ ] ]
--output / -O
the output bam
R String null
--output-shard-tmp-dir / NA
when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used
Exclusion: This argument cannot be used at the same time as sharded-output
.
String null
--program-name / NA
Name of the program running
String null
--QUIET / NA
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[String] []
--read-name-regex / NA
Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.
String
--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
String null
--remove-all-duplicates / NA
If true do not write duplicates to the output file instead of writing them with appropriate flags set.
Exclusion: This argument cannot be used at the same time as duplicate-tagging-policy, remove-sequencing-duplicates
.
boolean false
--remove-sequencing-duplicates / NA
If true do not write optical/sequencing duplicates to the output file instead of writing them with appropriate flags set.
Exclusion: This argument cannot be used at the same time as duplicate-tagging-policy, remove-all-duplicates
.
boolean false
--sharded-output / NA
For tools that write an output, write the output in multiple pieces (shards)
Exclusion: This argument cannot be used at the same time as output-shard-tmp-dir
.
boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--spark-master / NA
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
String local[*]
--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
--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
GATK version 4.1.0.0 built at Sat, 23 Nov 2019 17:12:18 -0500.
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