gatk4/gatk4_haplotypecaller

variant calling

germline

GATK

GATK4

SNV

indel

Description

Calls germline SNVs and indels via local re-assembly of haplotypes.

The HaplotypeCaller is capable of calling SNPs and indels simultaneously
via local de-novo assembly of haplotypes in an active region. Whenever
the program encounters a region showing signs of variation, it discards
the existing mapping information and completely reassembles the reads in
that region. This allows it to be more accurate when calling regions
that are traditionally difficult to call, for example when they contain
different types of variants close to each other.

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 call variants from. 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.

Name

Type & Properties

--input

-I

file

required

--bai

file

required

--reference

-R

file

required

--reference_fai

file

required

--reference_dict

file

required

Output

Name	Type & Properties	Description
--output -O	file required output	Output file containing the called variants. This can be a VCF file (`.vcf`/`.vcf.gz`) or, when `--emit_ref_confidence` is set to `GVCF`, a GVCF file.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--active_probability_threshold	double	Minimum probability for a locus to be considered active. Default: 0.002.
--activeregion_alt_multiplier	double	Multiplier for up-weighting ALT-supporting reads during active region determination. Default: 1.0.
--alleles	file	VCF file with the set of alleles to force-call regardless of evidence.
--annotation -A	string multiple	One or more specific annotations to add to variant calls, e.g. `ChromosomeCounts` or `InbreedingCoeff`.
--annotation_group -G	string multiple	One or more groups of annotations to apply to variant calls. Common values include `StandardAnnotation` and, for allele-specific annotations, `AS_StandardAnnotation`.
--annotations_to_exclude -AX	string multiple	One or more specific annotations to exclude from variant calls, e.g. `RMSMappingQuality` or `FisherStrand`.
--assembly_region_padding	integer	Number of additional bases of context to include around each assembly region. Default: 100.
--base_quality_score_threshold	integer	Base qualities below this threshold will be reduced to the minimum (6). Default: 18.
--contamination_fraction_to_filter -contamination	double	Fraction of contamination in sequencing data (for all samples) to aggressively remove. Default: 0.0.
--dbsnp -D	file	dbSNP VCF file used to annotate called variants with known variant IDs.
--disable_optimizations	boolean_true	Don't skip calculations in assembly regions with no variants.
--dont_use_soft_clipped_bases	boolean_true	Do not analyze soft-clipped bases in the reads.
--emit_ref_confidence -ERC	string	Mode for emitting reference confidence scores. Set this to `GVCF` to generate a GVCF file suitable for joint genotyping of multiple samples (e.g. via `gatk4 GenotypeGVCFs`). Default: 'NONE'.
--floor_blocks	boolean_true	Output the band lower bound for each GQ block regardless of the data it represents. Only relevant when `--emit_ref_confidence` is set to `GVCF`.
--force_active	boolean_true	If set, all regions are marked as active, disabling the active region detection step.
--founder_id	string multiple	Samples representing the population "founders", used together with `--pedigree` to inform genotyping priors.
--gvcf_gq_bands -GQB	integer multiple	Exclusive upper bounds for reference confidence GQ bands (must be in `[1, 100]` and specified in increasing order). Only relevant when `--emit_ref_confidence` is set to `GVCF`.
--heterozygosity	double	Expected heterozygosity value used to compute the prior probability of a het genotype. Default: 0.001.
--heterozygosity_stdev	double	Standard deviation of heterozygosity for SNP and indel calling. Default: 0.01.
--indel_heterozygosity	double	Heterozygosity for indel calling. Default: 0.000125.
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--kmer_size	integer multiple	Kmer size(s) to use in the read threading assembler. Default: 10, 25.
--max_alternate_alleles	integer	Maximum number of alternate alleles to genotype. Default: 6.
--max_assembly_region_size	integer	Maximum size of an assembly region. Default: 300.
--max_reads_per_alignment_start	integer	Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to `0` to disable. Default: 50.
--min_assembly_region_size	integer	Minimum size of an assembly region. Default: 50.
--min_base_quality_score -mbq	integer	Minimum base quality required to consider a base for calling. Default: 10.
--min_pruning	integer	Minimum support to not prune paths in the assembly graph. Default: 2.
--minimum_mapping_quality	integer	Minimum mapping quality required to consider a read for calling. Default: 20.
--output_mode	string	Specifies which type of calls to output. Default: 'EMIT_VARIANTS_ONLY'.
--pcr_indel_model	string	The PCR indel model to use. Set this parameter to `NONE` to disable the PCR indel model, for example when using PCR-free sequencing data. Default: 'CONSERVATIVE'.
--pedigree -ped	file	Pedigree file for determining the population "founders" (see `--founder_id`).
--ploidy_regions	file	Interval file with a column specifying the desired ploidy for genotyping models, overriding the default ploidy (and `--sample_ploidy`) in specific regions (e.g. sex chromosomes).
--sample_name -ALIAS	string	Name of a single sample to use from a multi-sample BAM file.
--sample_ploidy -ploidy	integer	Ploidy (number of chromosomes) per sample. For pooled data, set to (number of samples in each pool * sample ploidy). Default: 2.
--stand_call_conf -stand-call-conf	double	The minimum phred-scaled confidence threshold at which variants should be called. Default: 30.

Name

Type & Properties

--active_probability_threshold

double

--activeregion_alt_multiplier

double

--alleles

file

--annotation

-A

string

multiple

--annotation_group

-G

string

multiple

--annotations_to_exclude

-AX

string

multiple

--assembly_region_padding

integer

--base_quality_score_threshold

integer

--contamination_fraction_to_filter

-contamination

double

--dbsnp

-D

file

--disable_optimizations

boolean_true

--dont_use_soft_clipped_bases

boolean_true

--emit_ref_confidence

-ERC

string

--floor_blocks

boolean_true

--force_active

boolean_true

--founder_id

string

multiple

--gvcf_gq_bands

-GQB

integer

multiple

--heterozygosity

double

--heterozygosity_stdev

double

--indel_heterozygosity

double

--intervals

-L

file

--kmer_size

integer

multiple

--max_alternate_alleles

integer

--max_assembly_region_size

integer

--max_reads_per_alignment_start

integer

--min_assembly_region_size

integer

--min_base_quality_score

-mbq

integer

--min_pruning

integer

--minimum_mapping_quality

integer

--output_mode

string

--pcr_indel_model

string

--pedigree

-ped

file

--ploidy_regions

file

--sample_name

-ALIAS

string

--sample_ploidy

-ploidy

integer

--stand_call_conf

-stand-call-conf

double

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.vcf"  
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_haplotypecaller/main.nf \  
  -params-file params.yaml

gatk4/gatk4_haplotypecaller

GATK Engine Options

Input

Output

Options

Run this component

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