Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark

Category Read Data Manipulation

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Overview

The full BQSR pipeline in one tool to run on Spark. The final result is analysis-ready reads. This runs BaseRecalibrator and then ApplyBQSR to give a BAM with recalibrated base qualities.

Input

• A BAM or CRAM file containing input read data
• A database of known polymorphic sites to skip over.

Output

A BAM or CRAM file containing the recalibrated read data

Usage example

 gatk BQSRPipelineSpark \
   -R gs://my-gcs-bucket/reference.fasta \
   -I gs://my-gcs-bucket/input.bam \
   --known-sites gs://my-gcs-bucket/sites_of_variation.vcf \
   --known-sites gs://my-gcs-bucket/another/optional/setOfSitesToMask.vcf \
   -O gs://my-gcs-bucket/output.bam \
   -- \
   --sparkRunner GCS \
   --cluster my-dataproc-cluster
 

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Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by BQSRPipelineSpark.

• WellformedReadFilter

BQSRPipelineSpark 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
--known-sites	[]	the known variants
--output  -O	null	the output bam
--reference  -R	null	Reference sequence file
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).
--binary-tag-name	null	the binary tag covariate name if using it
--bqsr-baq-gap-open-penalty	40.0	BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets
--conf	[]	Spark properties to set on the Spark context in the format =
--default-base-qualities	-1	Assign a default base quality
--deletions-default-quality	45	default quality for the base deletions covariate
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--emit-original-quals	false	Emit original base qualities under the OQ tag
--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.
--global-qscore-prior	-1.0	Global Qscore Bayesian prior to use for BQSR
--help  -h	false	display the help message
--indels-context-size  -ics	3	Size of the k-mer context to be used for base insertions and deletions
--insertions-default-quality	45	default quality for the base insertions covariate
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L	[]	One or more genomic intervals over which to operate
--low-quality-tail	2	minimum quality for the bases in the tail of the reads to be considered
--maximum-cycle-value  -max-cycle	500	The maximum cycle value permitted for the Cycle covariate
--mismatches-context-size  -mcs	2	Size of the k-mer context to be used for base mismatches
--mismatches-default-quality	-1	default quality for the base mismatches covariate
--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
--preserve-qscores-less-than	6	Don't recalibrate bases with quality scores less than this threshold (with -bqsr)
--program-name	null	Name of the program running
--quantize-quals	0	Quantize quality scores to a given number of levels
--quantizing-levels	16	number of distinct quality scores in the quantized output
--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.
--spark-verbosity	null	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.)
--use-original-qualities  -OQ	false	Use the base quality scores from the OQ tag
--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
--round-down-quantized	false	Round quals down to nearest quantized qual
--showHidden	false	display hidden arguments
--static-quantized-quals	[]	Use static quantized quality scores to a given number of levels (with -bqsr)

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  [ [ -∞  ∞ ] ]

---

--binary-tag-name / NA

the binary tag covariate name if using it
The tag name for the binary tag covariate (if using it)

String  null

---

--bqsr-baq-gap-open-penalty / NA

BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets

double  40.0  [ [ -∞  ∞ ] ]

---

--conf / NA

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

---

--default-base-qualities / NA

Assign a default base quality
If reads are missing some or all base quality scores, this value will be used for all base quality scores. By default this is set to -1 to disable default base quality assignment.

byte  -1  [ [ -∞  ∞ ] ]

---

--deletions-default-quality / NA

default quality for the base deletions covariate
A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off. [default is on]

byte  45  [ [ -∞  ∞ ] ]

---

--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

---

--emit-original-quals / NA

Emit original base qualities under the OQ tag
The tool is capable of writing out the original quality scores of each read in the recalibrated output file under the "OQ" tag. By default, this behavior is disabled because emitting original qualities results in a significant increase of the file size. Use this flag to turn on emission of original qualities.

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  ""

---

--global-qscore-prior / NA

Global Qscore Bayesian prior to use for BQSR
If specified, the value of this argument will be used as a flat prior for all mismatching quality scores instead of the reported quality score (assigned by the sequencer).

double  -1.0  [ [ -∞  ∞ ] ]

---

--help / -h

display the help message

boolean  false

---

--indels-context-size / -ics

Size of the k-mer context to be used for base insertions and deletions
The context covariate will use a context of this size to calculate its covariate value for base insertions and deletions. Must be between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.

int  3  [ [ -∞  ∞ ] ]

---

--input / -I

BAM/SAM/CRAM file containing reads

R List[String]  []

---

--insertions-default-quality / NA

default quality for the base insertions covariate
A default base qualities to use as a prior (reported quality) in the insertion covariate model. This parameter is used for all reads without insertion quality scores for each base. [default is on]

byte  45  [ [ -∞  ∞ ] ]

---

--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]  []

---

--known-sites / NA

the known variants

R List[String]  []

---

--low-quality-tail / NA

minimum quality for the bases in the tail of the reads to be considered
Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter defines the quality below which (inclusive) a tail is considered low quality

byte  2  [ [ -∞  ∞ ] ]

---

--maximum-cycle-value / -max-cycle

The maximum cycle value permitted for the Cycle covariate
The cycle covariate will generate an error if it encounters a cycle greater than this value. This argument is ignored if the Cycle covariate is not used.

int  500  [ [ -∞  ∞ ] ]

---

--mismatches-context-size / -mcs

Size of the k-mer context to be used for base mismatches
The context covariate will use a context of this size to calculate its covariate value for base mismatches. Must be between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.

int  2  [ [ -∞  ∞ ] ]

---

--mismatches-default-quality / NA

default quality for the base mismatches covariate
A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off. [default is off]

byte  -1  [ [ -∞  ∞ ] ]

---

--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

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

---

--preserve-qscores-less-than / NA

Don't recalibrate bases with quality scores less than this threshold (with -bqsr)
This flag tells GATK not to modify quality scores less than this value. Instead they will be written out unmodified in the recalibrated BAM file. In general it's unsafe to change qualities scores below < 6, since base callers use these values to indicate random or bad bases. For example, Illumina writes Q2 bases when the machine has really gone wrong. This would be fine in and of itself, but when you select a subset of these reads based on their ability to align to the reference and their dinucleotide effect, your Q2 bin can be elevated to Q8 or Q10, leading to issues downstream.

int  6  [ [ -∞  ∞ ] ]

---

--program-name / NA

Name of the program running

String  null

---

--quantize-quals / NA

Quantize quality scores to a given number of levels
Turns on the base quantization module. It requires a recalibration report. A value of 0 here means "do not quantize". Any value greater than zero will be used to recalculate the quantization using that many levels. Negative values mean that we should quantize using the recalibration report's quantization level.

Exclusion: This argument cannot be used at the same time as static-quantized-quals, round-down-quantized.

int  0  [ [ -∞  ∞ ] ]

---

--quantizing-levels / NA

number of distinct quality scores in the quantized output
BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base qualities, this is done by the engine with the -qq or -bqsr options. This parameter tells BQSR the number of levels of quantization to use to build the quantization table.

int  16  [ [ -∞  ∞ ] ]

---

--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 file

R String  null

---

--round-down-quantized / NA

Round quals down to nearest quantized qual
Round down quantized only works with the static_quantized_quals option, and should not be used with the dynamic binning option provided by quantize_quals. When roundDown = false, rounding is done in probability space to the nearest bin. When roundDown = true, the value is rounded to the nearest bin that is smaller than the current bin.

Exclusion: This argument cannot be used at the same time as quantize-quals.

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[*]

---

--spark-verbosity / NA

Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}

String  null

---

--static-quantized-quals / NA

Use static quantized quality scores to a given number of levels (with -bqsr)
Static quantized quals are entirely separate from the quantize_qual option which uses dynamic binning. The two types of binning should not be used together.

Exclusion: This argument cannot be used at the same time as quantize-quals.

List[Integer]  []

---

--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  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 / NA

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

---

--use-original-qualities / -OQ

Use the base quality scores from the OQ tag
This flag tells GATK to use the original base qualities (that were in the data before BQSR/recalibration) which are stored in the OQ tag, if they are present, rather than use the post-recalibration quality scores. If no OQ tag is present for a read, the standard qual score will be used.

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

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GATK version 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.