gatk4/gatk4_applybqsr

BQSR

base quality recalibration

GATK

GATK4

alignment

Description

Apply a linear base quality recalibration model trained with the
BaseRecalibrator tool.

This is the second pass of the GATK Base Quality Score Recalibration
(BQSR) workflow. It applies the recalibration table produced by
gatk4_baserecalibrator to the input BAM, adjusting base quality scores
to correct for systematic technical errors in the sequencing process.

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.
--bqsr_recal_file -bqsr	file required	Input recalibration table for BQSR, as produced by `gatk BaseRecalibrator`.
--reference -R	file	Reference sequence FASTA file. If provided, `--reference_fai` and `--reference_dict` must be provided too.
--reference_fai	file	FASTA index file (`.fai`) for the reference sequence.
--reference_dict	file	Sequence dictionary (`.dict`) file for the reference sequence.

Name

Type & Properties

--input

-I

file

required

--bai

file

required

--bqsr_recal_file

-bqsr

file

required

--reference

-R

file

--reference_fai

file

--reference_dict

file

Output

Name	Type & Properties	Description
--output -O	file required output	Recalibrated output BAM file.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--allow_missing_read_group	boolean_true	Do not throw an error when encountering a read group in the input BAM that is not in the recalibration table.
--emit_original_quals	boolean_true	Emit the original base qualities under the `OQ` tag, alongside the recalibrated qualities.
--exclude_intervals -XL	file	One or more genomic intervals to exclude from processing, provided as a file (e.g. BED, interval_list).
--global_qscore_prior	double	Global Q-score Bayesian prior to use for BQSR. A negative value disables this behavior. Default: -1.0.
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--preserve_qscores_less_than	integer	Don't recalibrate bases with quality scores less than this threshold. Default: 6.
--quantize_quals	integer	Quantize quality scores to a given number of levels. Set to `0` to disable quantization. Default: 0. Mutually exclusive with `--static_quantized_quals`.
--round_down_quantized	boolean_true	Round quantized quality scores down to the nearest quantized value. Cannot be used with `--quantization_levels`.
--static_quantized_quals	integer multiple	Use static quantized quality scores to a given number of levels. Can be specified multiple times to define several levels, each producing one `--static-quantized-quals` flag passed to the tool. Mutually exclusive with `--quantize_quals`.
--use_original_qualities -OQ	boolean_true	Use the original base quality scores (`OQ` tag) from the input BAM instead of the current ones.

Name

Type & Properties

--allow_missing_read_group

boolean_true

--emit_original_quals

boolean_true

--exclude_intervals

-XL

file

--global_qscore_prior

double

--intervals

-L

file

--preserve_qscores_less_than

integer

--quantize_quals

integer

--round_down_quantized

boolean_true

--static_quantized_quals

integer

multiple

--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.bam"  
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_applybqsr/main.nf \  
  -params-file params.yaml

gatk4/gatk4_applybqsr

GATK Engine Options

Input

Output

Options

Run this component

Relationships

Used by

Uses