gatk4/gatk4_combinegvcfs

variant calling

germline

GATK

GATK4

GVCF

joint genotyping

Description

Merges multiple per-sample GVCF files (produced by gatk4 HaplotypeCaller
in --emit_ref_confidence GVCF mode) into a single multi-sample GVCF with
appropriate annotations.

The resulting combined GVCF is not genotyped, it is intended to be used
as input to gatk4 GenotypeGVCFs to jointly call genotypes across all
merged samples.

Type

bash_script

License

Apache-2.0

Keywords

variant calling

germline

GATK

GATK4

GVCF

joint genotyping

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_combinegvcfs/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 multiple	Per-sample GVCF file(s) to combine (as produced by `gatk4 HaplotypeCaller` in `--emit_ref_confidence GVCF` mode). Specify this argument once per input GVCF 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

--variant

-V

file

required

multiple

--reference

-R

file

required

--reference_fai

file

required

--reference_dict

file

required

Output

Name	Type & Properties	Description
--output -O	file required output	The combined multi-sample GVCF output file.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--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.
--annotations_to_exclude -AX	string multiple	One or more specific annotations to exclude from variant calls
--break_bands_at_multiples_of	integer	If greater than `0`, reference bands will be broken up at genomic positions that are multiples of this number. Default: 0.
--call_genotypes	boolean_true	Output called genotypes.
--combine_variants_distance	integer	Maximum distance (in bp) for variants to be grouped together when combining. Default: 0.
--convert_to_base_pair_resolution	boolean_true	If specified, convert banded GVCFs to all-sites GVCFs.
--dbsnp -D	file	dbSNP VCF file used to annotate the combined GVCF with known variant IDs.
--disable_tool_default_annotations	boolean_true	Disable all tool default annotations.
--drop_somatic_filtering_annotations	boolean_true	For input somatic GVCFs (i.e. from Mutect2), drop filtering annotations.
--enable_all_annotations	boolean_true	Use all possible annotations (not for the faint of heart).
--founder_id	string multiple	Samples representing the population "founders", used (together with `--pedigree`) by pedigree-aware annotations.
--ignore_variants_starting_outside_interval	boolean_true	Restrict variant output to sites that start within the provided `--intervals` (only applies when an interval is specified).
--input_is_somatic	boolean_true	Merge input GVCFs according to somatic (i.e. Mutect2) annotations (BETA).
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--max_variants_per_shard	integer	If non-zero, partitions VCF output into shards, each containing up to the given number of records. Default: 0.
--pedigree -ped	file	Pedigree file for determining the population "founders".
--ref_padding	integer	Number of bases on either side to expand the spanning reference window. Default: 1.
--variant_output_filtering	string	Restrict the output variants to ones that match the `--intervals` according to the specified matching mode.

Name

Type & Properties

--annotation

-A

string

multiple

--annotation_group

-G

string

multiple

--annotations_to_exclude

-AX

string

multiple

--break_bands_at_multiples_of

integer

--call_genotypes

boolean_true

--combine_variants_distance

integer

--convert_to_base_pair_resolution

boolean_true

--dbsnp

-D

file

--disable_tool_default_annotations

boolean_true

--drop_somatic_filtering_annotations

boolean_true

--enable_all_annotations

boolean_true

--founder_id

string

multiple

--ignore_variants_starting_outside_interval

boolean_true

--input_is_somatic

boolean_true

--intervals

-L

file

--max_variants_per_shard

integer

--pedigree

-ped

file

--ref_padding

integer

--variant_output_filtering

string