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**BETA** ApplyBQSRSpark

Apply base quality score recalibration on Spark

Category Read Data Manipulation


Overview

Apply base quality score recalibration with Spark.

This tool performs the second pass in a two-stage process called Base Quality Score Recalibration (BQSR). Specifically, it recalibrates the base qualities of the input reads based on the recalibration table produced by the BaseRecalibrator tool, and outputs a recalibrated BAM or CRAM file.

See Tutorial#10060 for an example of how to set up and run a Spark tool on a cloud Spark cluster.

Usage examples

 gatk ApplyBQSRSpark \
 -I gs://my-gcs-bucket/input.bam \
 -bqsr gs://my-gcs-bucket/recalibration.table \
 -O gs://my-gcs-bucket/output.bam \
 -- \
 --sparkRunner GCS \
 --cluster my-dataproc-cluster
 

To additionally bin base qualities:

 gatk ApplyBQSRSpark \
 -I gs://my-gcs-bucket/input.bam \
 -bqsr gs://my-gcs-bucket/recalibration.table \
 --static-quantized-quals 10 --static-quantized-quals 20 \
 --static-quantized-quals 30 --static-quantized-quals 40 \
 -O gs://my-gcs-bucket/output.bam \
 -- \
 --sparkRunner GCS \
 --cluster my-dataproc-cluster
 

Additional Information

Read filters

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

ApplyBQSRSpark 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
--bqsr-recal-file
 -bqsr
null Input covariates table file for base quality score recalibration
--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!
--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
--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
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
--program-name
null Name of the program running
--quantize-quals
0 Quantize quality scores to a given number of levels
--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.
--spark-verbosity
null Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
--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  [ [ -∞  ∞ ] ]


--bqsr-recal-file / -bqsr

Input covariates table file for base quality score recalibration
Enables recalibration of base qualities. The covariates tables are produced by the BaseRecalibrator tool. Please be aware that you should only run recalibration with the covariates file created on the same input bam(s).

R String  null


--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


--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


--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]  []


--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
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  [ [ -∞  ∞ ] ]


--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


--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-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 quality 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 4.1.2.0 built at Tue, 23 Apr 2019 14:55:55 -0400.