SortSam on Spark (works on SAM/BAM/CRAM)
Category Read Data Manipulation
Overview
SortSam on Spark (works on SAM/BAM/CRAM)A Spark implementation of Picard SortSam. The Spark version can 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. See Blog#23420 for performance benchmarks.
The tool sorts reads by coordinate order by default or alternatively by read name, the QNAME field, if asked with the '-SO queryname' option. The contig ordering in the reference dictionary defines coordinate order, and the tool uses the sequence dictionary represented by the @SQ header lines or that of the optionally provided reference to sort reads by the RNAME field. For those reads mapping to a contig, coordinate sorting further orders reads by the POS field of the SAM record, which contains the leftmost mapping position.
To queryname-sort, the tool first groups by readname and then deterministically sorts within a readname set by orientation, secondary and supplementary SAM flags. For paired-end reads, reads in the pair share the same queryname. Because aligners can generate secondary and supplementary alignments, queryname groups can consists of, e.g. more than two records for a paired-end pair.
Usage examples
Coordinate-sort aligned reads using all cores available locallygatk SortSamSpark \ -I aligned.bam \ -O coordinatesorted.bamQueryname-sort reads using four cores on a Spark cluster
gatk SortSamSpark \ -I coordinatesorted.bam \ -SO queryname \ -O querygroupsorted.bam \ -- \ --spark-runner SPARK \ --spark-master \ --num-executors 5 \ --executor-cores 4
Notes
- This Spark tool requires a significant amount of disk operations. Run with both the input data and outputs on high throughput SSDs when possible. When pipelining this tool on Google Compute Engine instances, for best performance requisition machines with LOCAL SSDs.
- Furthermore, we recommend explicitly setting the Spark temp directory to an available SSD when running this in local mode by adding the argument --conf 'spark.local.dir=/PATH/TO/TEMP/DIR'. See the discussion at https://gatkforums.broadinstitute.org/gatk/discussion/comment/56337 for details.
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by SortSamSpark.
SortSamSpark 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 |
the output file path | ||
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! | |
--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 | ||
--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. | |
--output-shard-tmp-dir |
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 |
Name of the program running | ||
--reference -R |
Reference sequence | ||
--sharded-output |
false | For tools that write an output, write the output in multiple pieces (shards) | |
--sort-order -SO |
coordinate | sort order of the output file | |
--spark-master |
local[*] | URL of the Spark Master to submit jobs to when using the Spark pipeline runner. | |
--spark-verbosity |
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE} | ||
--use-nio |
false | Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.) | |
--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 |
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. | |
--splitting-index-granularity |
4096 | Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points. | |
--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-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] []
--bam-partition-size
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
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
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
--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
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
R 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] []
--num-reducers
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 [ [ -∞ ∞ ] ]
--output / -O
the output file path
R String null
--output-shard-tmp-dir
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
Name of the program running
String 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
GATKPath null
--sharded-output
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
--sort-order / -SO
sort order of the output file
The --sort-order argument is an enumerated type (SparkSortOrder), which can have one of the following values:
- coordinate
- queryname
SparkSortOrder coordinate
--spark-master
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
String local[*]
--spark-verbosity
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
String null
--splitting-index-granularity
Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points.
long 4096 [ [ 1 ∞ ] ]
--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
--use-nio
Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.)
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 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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