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**BETA** CollectInsertSizeMetricsSpark

Collects insert size distribution information on alignment data

Category Diagnostics and Quality Control


Overview

Collects insert size distribution information in alignment data. The tool leverages the Spark framework for faster operation.

Usage example

 gatk CollectInsertSizeMetricsSpark \
   -I gs://cloud-bucket/input.bam \
   -H gs://cloud-bucket/insert_size_histogram.pdf \
   -O gs://cloud-bucket/insert_size_metrics.txt \
   -- \
   --spark-runner GCS \
   --cluster my-dataproc-cluster
 

See http://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics for an explanation of individual metrics. See Tutorial#10060 for an example of how to set up and run a Spark tool on a cloud Spark cluster.


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by CollectInsertSizeMetricsSpark.

CollectInsertSizeMetricsSpark 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
--histogram-plot-file
 -H
null File to write insert size histogram chart to.
--input
 -I
[] BAM/SAM/CRAM file containing reads
--output
 -O
null File to write the output to.
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.
--help
 -h
false display the help message
--histogram-plot-deviations-tolerance
 -TOL
10.0 Generate mean, sd and plots by trimming the data down to MEDIAN + maxMADTolerance*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and sd grossly misleading regarding the real distribution.
--interval-merging-rule
 -imr
ALL Interval merging rule for abutting intervals
--intervals
 -L
[] One or more genomic intervals over which to operate
--metric-accumulation-level
 -LEVEL
[ALL_READS] The level(s) at which to accumulate metrics. Possible values are {ALL_READS, SAMPLE, LIBRARY, READ GROUP}.
--min-category-reads-percentage
 -M
0.05 When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads (Range: 0 to 1).
--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
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
--produce-plot
false If enabled, an output .pdf plot will be created.
--program-name
null Name of the program running
--reference
 -R
null Reference sequence
--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
--width
 -W
null Explicitly sets the histogram width, overriding automatic truncation of Histogram tail. Also, when calculating mean and standard deviation, only bins <= HISTOGRAM_WIDTH will be included.
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


--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


--histogram-plot-deviations-tolerance / -TOL

Generate mean, sd and plots by trimming the data down to MEDIAN + maxMADTolerance*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and sd grossly misleading regarding the real distribution.

double  10.0  [ [ -∞  ∞ ] ]


--histogram-plot-file / -H

File to write insert size histogram chart to.

R String  null


--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]  []


--metric-accumulation-level / -LEVEL

The level(s) at which to accumulate metrics. Possible values are {ALL_READS, SAMPLE, LIBRARY, READ GROUP}.

Set[MetricAccumulationLevel]  [ALL_READS]


--min-category-reads-percentage / -M

When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads (Range: 0 to 1).

float  0.05  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--output / -O

File to write the output to.

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


--produce-plot / NA

If enabled, an output .pdf plot will be created.

boolean  false


--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-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


--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


--width / -W

Explicitly sets the histogram width, overriding automatic truncation of Histogram tail. Also, when calculating mean and standard deviation, only bins <= HISTOGRAM_WIDTH will be included.

Integer  null


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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.