Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark
Category Read Data Manipulation
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
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by BQSRPipelineSpark.
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 |
the output bam | ||
--reference -R |
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 |
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. User must have storage.buckets.get permission on the bucket being 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 |
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 |
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 |
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 |
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 | |||
--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
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 [ [ -∞ ∞ ] ]
--binary-tag-name
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
BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets
double 40.0 [ [ -∞ ∞ ] ]
--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
--default-base-qualities
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
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
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
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 ""
--global-qscore-prior
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[GATKPath] []
--insertions-default-quality
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
the known variants
R List[String] []
--low-quality-tail
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
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
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
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
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
Name of the program running
String null
--quantize-quals
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
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
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 file
R GATKPath null
--round-down-quantized
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
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
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 ∞ ] ]
--static-quantized-quals
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
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
--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
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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