Generates recalibration table for Base Quality Score Recalibration (BQSR)

Category Read Data Manipulation

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Overview

First pass of the base quality score recalibration. Generates a recalibration table based on various covariates. The default covariates are read group, reported quality score, machine cycle, and nucleotide context.

This walker generates tables based on specified covariates. It does a by-locus traversal operating only at sites that are in the known sites VCF. ExAc, gnomAD, or dbSNP resources can be used as known sites of variation. We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. Since there is a large amount of data one can then calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations. The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score).

Input

The input read data whose base quality scores need to be assessed.

A database of known polymorphic sites to skip over.

Output

A GATK Report file with many tables:

1. The list of arguments
2. The quantized qualities table
3. The recalibration table by read group
4. The recalibration table by quality score
5. The recalibration table for all the optional covariates

The GATK Report is intended to be easy to read by humans or computers. Check out the documentation of the GATKReport to learn how to manipulate this table.

Examples

 gatk BaseRecalibrator \
   -I my_reads.bam \
   -R reference.fasta \
   --known-sites sites_of_variation.vcf \
   --known-sites another/optional/setOfSitesToMask.vcf \
   -O recal_data.table
 

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Additional Information

Read filters

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

• NotSecondaryAlignmentReadFilter
• PassesVendorQualityCheckReadFilter
• MappedReadFilter
• MappingQualityAvailableReadFilter
• NotDuplicateReadFilter
• MappingQualityNotZeroReadFilter
• WellformedReadFilter

BaseRecalibrator 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		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.
--output  -O		The output recalibration table file to create
--reference  -R		Reference sequence file
Optional Tool Arguments
--arguments_file		read one or more arguments files and add them to the command line
--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
--cloud-index-prefetch-buffer  -CIPB	-1	Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloud-prefetch-buffer  -CPB	40	Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--default-base-qualities	-1	Assign a default base quality
--deletions-default-quality	45	default quality for the base deletions covariate
--disable-bam-index-caching  -DBIC	false	If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
--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
--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
--preserve-qscores-less-than	6	Don't recalibrate bases with quality scores less than this threshold (with -bqsr)
--quantizing-levels	16	number of distinct quality scores in the quantized output
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--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-sam-program-record	true	If true, adds a PG tag to created SAM/BAM/CRAM files.
--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/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5  -OBM	false	If true, create a MD5 digest for any BAM/SAM/CRAM file created
--create-output-variant-index  -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5  -OVM	false	If true, create a a MD5 digest any VCF file created.
--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
--lenient  -LE	false	Lenient processing of VCF files
--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.
--seconds-between-progress-updates	10.0	Output traversal statistics every time this many seconds elapse
--sequence-dictionary		Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--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.

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--add-output-sam-program-record / -add-output-sam-program-record

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true

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--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean  true

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--arguments_file

read one or more arguments files and add them to the command line

List[File]  []

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--binary-tag-name

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

String  null

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--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  [ [ -∞  ∞ ] ]

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--cloud-index-prefetch-buffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]

---

--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]

---

--create-output-bam-index / -OBI

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean  true

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--create-output-bam-md5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false

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--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

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--create-output-variant-md5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean  false

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--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  [ [ -∞  ∞ ] ]

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--disable-bam-index-caching / -DBIC

If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.

boolean  false

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--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

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--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]  []

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--gatk-config-file

A configuration file to use with the GATK.

String  null

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--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  ""

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--help / -h

display the help message

boolean  false

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--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  [ [ -∞  ∞ ] ]

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--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  [ [ -∞  ∞ ] ]

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--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  [ [ -∞  ∞ ] ]

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--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

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--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  [ [ -∞  ∞ ] ]

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--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

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--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

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--known-sites

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.
This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference, so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of Feature-containing files (VCF, BCF, BED, etc.) for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites. Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument.

R List[FeatureInput[Feature]]  []

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

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--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  [ [ -∞  ∞ ] ]

---

--output / -O

The output recalibration table file to create
After the header, data records occur one per line until the end of the file. The first several items on a line are the values of the individual covariates and will change depending on which covariates were specified at runtime. The last three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches, and the raw empirical quality score calculated by phred-scaling the mismatch rate. Use '/dev/stdout' to print to standard out.

R File  null

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--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  [ [ -∞  ∞ ] ]

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--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

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--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

---

--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

String  null

---

--showHidden / -showHidden

display hidden arguments

boolean  false

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--sites-only-vcf-output

If true, don't emit genotype fields when writing vcf file output.

boolean  false

---

--tmp-dir

Temp directory to use.

GATKPath  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--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

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--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

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--version

display the version number for this tool

boolean  false

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GATK version 4.1.9.0-SNAPSHOT built at Mon, 19 Oct 2020 11:41:12 -0400.