gatk4/gatk4_genotypegvcfs

variant calling

germline

joint genotyping

GATK

GATK4

VCF

GVCF

Description

Perform joint genotyping on one or more samples previously called with
HaplotypeCaller in GVCF mode.

GenotypeGVCFs merges the records in the input GVCF(s) and performs joint
genotyping to produce a set of final, genotyped calls in a VCF file. The
input can be a single-sample GVCF (e.g. from gatk4 HaplotypeCaller run
with --emit_ref_confidence GVCF), a combined multi-sample GVCF (e.g.
from gatk4 CombineGVCFs), or a GenomicsDB workspace produced by
gatk4 GenomicsDBImport.

Type

bash_script

License

Apache-2.0

Keywords

variant calling

germline

joint genotyping

GATK

GATK4

VCF

GVCF

Links

Repository

Documentation

Contributors

Launch

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_genotypegvcfs/main.nf \  
  -params-file params.yaml

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
--variant -V	file required	Input variants to joint-genotype. This can be one of: - A single-sample GVCF produced by `gatk4 HaplotypeCaller` run with `--emit_ref_confidence GVCF` - A combined multi-sample GVCF produced by `gatk4 CombineGVCFs` - A GenomicsDB workspace directory produced by `gatk4 GenomicsDBImport` When a directory is provided, it is assumed to be a GenomicsDB workspace and is automatically referenced with the required `gendb://` prefix.
--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

--variant

-V

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 final, genotyped variants in VCF format (`.vcf`/`.vcf.gz`).

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--allele_fraction_error	double	Margin of error in allele fraction to consider a somatic variant homoplasmic. Only relevant when `--input_is_somatic` is set. Default: 0.001.
--annotate_with_num_discovered_alleles	boolean_true	Annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site.
--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`.
--call_genotypes	boolean_true	Output called genotypes in the final VCF (otherwise no-call).
--dbsnp -D	file	dbSNP VCF file used to annotate called variants with known variant IDs.
--disable_tool_default_annotations	boolean_true	Disable all tool default annotations.
--enable_all_annotations	boolean_true	Use all possible annotations (not for the faint of heart).
--force_output_intervals	file multiple	Sites at which to output genotypes even if non-variant in all samples, provided as a file (e.g. BED, interval_list). Can be specified multiple times.
--founder_id	string multiple	Samples representing the population "founders", used (together with `--pedigree`) by pedigree-aware genotype assignment (see `--genotype_assignment_method`).
--genomicsdb_max_alternate_alleles	integer	Maximum number of alternate alleles that will be combined when reading variants from a GenomicsDB workspace. Default: 50.
--genomicsdb_shared_posixfs_optimizations	boolean_true	Allow optimizations to improve the usability and performance of reading a GenomicsDB workspace on shared POSIX filesystems (e.g. NFS, Lustre). Disables file-level locking and minimizes file system writes.
--genomicsdb_use_bcf_codec	boolean_true	Use BCF codec streaming for data read from a GenomicsDB workspace instead of the default VCF codec. Performs slightly better, but does not support 64-bit positions or very large `INFO` field sizes.
--genotype_assignment_method -gam	string	How genotypes are assigned in the final VCF. Default: 'USE_PLS_TO_ASSIGN'.
--heterozygosity	double	Heterozygosity value used to compute prior probabilities for any locus. See the [GATK docs](https://gatk.broadinstitute.org/hc/en-us) for full details on the meaning of this population genetics concept. Default: 0.001.
--heterozygosity_stdev	double	Standard deviation of heterozygosity for SNP and indel calling. Default: 0.01.
--include_non_variant_sites -all-sites	boolean_true	Include loci found to be non-variant after genotyping in the output.
--indel_heterozygosity	double	Heterozygosity for indel calling. See the [GATK docs](https://gatk.broadinstitute.org/hc/en-us) for full details on the meaning of this population genetics concept. Default: 0.000125.
--input_is_somatic	boolean_true	Finalize the input GVCF according to somatic (i.e. Mutect2) TLODs (BETA feature).
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--keep_combined_raw_annotations -keep-combined	boolean_true	Keep the combined raw annotations. Cannot be used together with `--keep_specific_combined_raw_annotation`.
--keep_specific_combined_raw_annotation -keep-specific-combined	string multiple	Keep only the specific combined raw annotations specified (removing the other raw annotations). Cannot be used together with `--keep_combined_raw_annotations`.
--max_alternate_alleles	integer	Maximum number of alternate alleles to genotype. Default: 6.
--max_genotype_count	integer	Maximum number of genotypes to consider at any site. Default: 1024.
--max_variants_per_shard	integer	If non-zero, partitions VCF output into shards, each containing up to the given number of records. Default: 0.
--merge_input_intervals	boolean_true	Import all data in between intervals rather than only the intervals themselves.
--num_reference_samples_if_no_call	integer	Number of hom-ref genotypes to infer at sites not present in a `--population_callset` panel. Default: 0.
--only_output_calls_starting_in_intervals	boolean_true	Restrict variant output to sites that start within the provided `--intervals`.
--pedigree -ped	file	Pedigree file for determining the population "founders" (see `--founder_id`).
--population_callset -population	file	Callset (VCF) used to calculate genotype priors. Used together with `--num_reference_samples_if_no_call` and `--use_posteriors_to_calculate_qual`.
--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.
--somatic_quality_threshold	double	SQ (somatic quality) threshold to emit a variant to the VCF. Only relevant when `--input_is_somatic` is set. Default: 3.0.
--stand_call_conf -stand-call-conf	double	The minimum phred-scaled confidence threshold at which variants should be called. Default: 30.0.
--tumor_lod_to_emit -emit-lod	double	LOD threshold to emit a variant to the VCF. Only relevant when `--input_is_somatic` is set. Default: 3.5.
--use_posteriors_to_calculate_qual -gp-qual	boolean_true	If available, use the genotype posterior probabilities (see `--population_callset`) to calculate the site QUAL.
--variant_output_filtering	string	Restrict the output variants to ones that match the `--intervals` according to the specified matching mode.

Name

Type & Properties

--allele_fraction_error

double

--annotate_with_num_discovered_alleles

boolean_true

--annotation

-A

string

multiple

--annotation_group

-G

string

multiple

--annotations_to_exclude

-AX

string

multiple

--call_genotypes

boolean_true

--dbsnp

-D

file

--disable_tool_default_annotations

boolean_true

--enable_all_annotations

boolean_true

--force_output_intervals

file

multiple

--founder_id

string

multiple

--genomicsdb_max_alternate_alleles

integer

--genomicsdb_shared_posixfs_optimizations

boolean_true

--genomicsdb_use_bcf_codec

boolean_true

--genotype_assignment_method

-gam

string

--heterozygosity

double

--heterozygosity_stdev

double

--include_non_variant_sites

-all-sites

boolean_true

--indel_heterozygosity

double

--input_is_somatic

boolean_true

--intervals

-L

file

--keep_combined_raw_annotations

-keep-combined

boolean_true

--keep_specific_combined_raw_annotation

-keep-specific-combined

string

multiple

--max_alternate_alleles

integer

--max_genotype_count

integer

--max_variants_per_shard

integer

--merge_input_intervals

boolean_true

--num_reference_samples_if_no_call

integer

--only_output_calls_starting_in_intervals

boolean_true

--pedigree

-ped

file

--population_callset

-population

file

--sample_ploidy

-ploidy

integer

--somatic_quality_threshold

double

--stand_call_conf

-stand-call-conf

double

--tumor_lod_to_emit

-emit-lod

double

--use_posteriors_to_calculate_qual

-gp-qual

boolean_true

--variant_output_filtering

string