gatk4/gatk4_baserecalibrator

base quality score recalibration

BQSR

GATK

GATK4

preprocessing

Description

First pass of the Base Quality Score Recalibration (BQSR) process.

Generates a recalibration table based on various user-specified
covariates (such as read group, reported quality score, machine cycle,
and nucleotide context), modeling systematic errors made by the
sequencing machine that cause it to over- or under-estimate the quality
scores assigned to each individual base call. Known sites of variation
are used to mask out bases at sites of real (expected) variation, so
that the model captures only errors. The resulting recalibration table
is consumed by gatk4 ApplyBQSR to recalibrate the base quality scores
in the original BAM file.

GATK Engine Options

Name	Type & Properties	Description
--interval_padding -ip	integer	Amount of padding (in bp) to add to each interval specified via `--intervals`, to capture flanking context (e.g. near capture/exome-bait edges). Default: 0. A commonly-used value in GATK's own exome workflows is `100`.
--sites_only_vcf_output	boolean_true	Only emit site-level information in the output VCF/GVCF, dropping the FORMAT/genotype columns. Useful for producing a compact, privacy-preserving sites-only VCF (e.g. for public release or QC).
--create_output_variant_index -OVI	boolean	Create a VCF index (`.tbi`) when writing a coordinate-sorted VCF output. Default: true.
--create_output_bam_index -OBI	boolean	Create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM output. Default: true.
--output_cram_version	string	CRAM version to write for CRAM output ('3.0' or '3.1'). Ignored for BAM/SAM output. Note that CRAM 3.1 cannot be read by tools that only support CRAM 3.0. Default: '3.1'.
--read_filter -RF	string multiple	Read filter(s) to apply before analysis, given by their GATK Java class name (e.g. `MappingQualityReadFilter`). Can be specified multiple times.
--disable_read_filter -DF	string multiple	Read filter(s) to disable before analysis, given by their GATK Java class name. Can be specified multiple times.
--disable_tool_default_read_filters	boolean_true	Disable all tool-default read filters. Many tools will not function correctly without their default read filters enabled, so use with caution.
--disable_sequence_dictionary_validation	boolean_true	Do not check the input sequence dictionaries for compatibility. Useful when combining files from different sources with mismatched (but compatible) dictionaries. Use at your own risk.

Name

Type & Properties

--interval_padding

-ip

integer

--sites_only_vcf_output

boolean_true

--create_output_variant_index

-OVI

boolean

--create_output_bam_index

-OBI

boolean

--output_cram_version

string

--read_filter

-RF

string

multiple

--disable_read_filter

-DF

string

multiple

--disable_tool_default_read_filters

boolean_true

--disable_sequence_dictionary_validation

boolean_true

Input

Name	Type & Properties	Description
--input -I	file required	Input BAM file containing reads to be recalibrated. The file must be coordinate-sorted and indexed (see `--bai`).
--bai	file required	BAM index file (`.bai`) for the input BAM file.
--reference -R	file required	Reference sequence FASTA file.
--reference_fai	file required	FASTA index file (`.fai`) for the reference sequence.
--reference_dict	file required	Sequence dictionary (`.dict`) file for the reference sequence.
--known_sites	file required multiple	One or more databases of known polymorphic sites (e.g. dbSNP, Mills and 1000G gold standard indels) used to exclude regions around known polymorphisms from the recalibration analysis. At least one known-sites VCF file must be provided.

Name

Type & Properties

--input

-I

file

required

--bai

file

required

--reference

-R

file

required

--reference_fai

file

required

--reference_dict

file

required

--known_sites

file

required

multiple

Output

Name	Type & Properties	Description
--output -O	file required output	Output recalibration table file (GATKReport format) to be used as input to `gatk4 ApplyBQSR`.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--binary_tag_name	string	The binary tag covariate name if using it.
--bqsr_baq_gap_open_penalty	double	BQSR BAQ gap open penalty (Phred scaled). Default: 40. `30` is perhaps better for whole genome call sets.
--default_base_qualities	integer	Assign a default base quality to use in place of read qualities that are missing or invalid. Default: -1.
--deletions_default_quality	integer	Default quality for the base deletions covariate. Default: 45.
--indels_context_size -ics	integer	Size of the k-mer context to be used for base insertions and deletions. Default: 3.
--insertions_default_quality	integer	Default quality for the base insertions covariate. Default: 45.
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--low_quality_tail	integer	Minimum quality for the bases in the tail of the reads to be considered. Default: 2.
--maximum_cycle_value -max-cycle	integer	The maximum cycle value permitted for the Cycle covariate. Default: 500.
--mismatches_context_size -mcs	integer	Size of the k-mer context to be used for base mismatches. Default: 2.
--mismatches_default_quality	integer	Default quality for the base mismatches covariate. Default: -1.
--preserve_qscores_less_than	integer	Don't recalibrate bases with quality scores less than this threshold. Default: 6.
--quantizing_levels	integer	Number of distinct quality scores in the quantized output. Default: 16.
--use_original_qualities -OQ	boolean_true	Use the base quality scores from the `OQ` tag instead of the current ones.

Name

Type & Properties

--binary_tag_name

string

--bqsr_baq_gap_open_penalty

double

--default_base_qualities

integer

--deletions_default_quality

integer

--indels_context_size

-ics

integer

--insertions_default_quality

integer

--intervals

-L

file

--low_quality_tail

integer

--maximum_cycle_value

-max-cycle

integer

--mismatches_context_size

-mcs

integer

--mismatches_default_quality

integer

--preserve_qscores_less_than

integer

--quantizing_levels

integer

--use_original_qualities

-OQ

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.table"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/gatk4/gatk4_baserecalibrator/main.nf \  
  -params-file params.yaml

gatk4/gatk4_baserecalibrator

GATK Engine Options

Input

Output

Options

Run this component

Relationships

Used by

Uses