gatk4/gatk4_selectvariants

variant selection

GATK

GATK4

VCF

filtering

Description

Selects a subset of variants from a VCF file based on various criteria.

This tool makes it possible to select a subset of variants based on
various criteria in order to facilitate certain analyses. Examples include
comparing and contrasting cases vs. controls, extracting variant or
non-variant loci that meet certain requirements, or troubleshooting some
unexpected results, to name a few.

Type

bash_script

License

Apache-2.0

Keywords

variant selection

GATK

GATK4

VCF

filtering

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.gz"  
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_selectvariants/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 VCF file containing variants to select from.
--reference -R	file	Reference genome FASTA file. Optional for `SelectVariants` itself, but if provided, `--reference_fai` and `--reference_dict` must be provided too.
--reference_fai	file	FASTA index (`.fai`) file for the reference genome.
--reference_dict	file	Sequence dictionary (`.dict`) file for the reference genome.

Name

Type & Properties

--variant

-V

file

required

--reference

-R

file

--reference_fai

file

--reference_dict

file

Output

Name	Type & Properties	Description
--output -O	file required output	Output VCF file containing the selected variants.

Name

Type & Properties

--output

-O

file

required

output

Options

Name	Type & Properties	Description
--apply_jexl_filters_first -jexl-first	boolean_true	Apply JEXL-based filtering (`--select_expressions`) before subsetting samples.
--call_genotypes	boolean_true	Output called genotypes in the final VCF (otherwise no-call).
--concordance -conc	file	Output variants that are also called in this comparison VCF track.
--discordance -disc	file	Output variants that are not called in this comparison VCF track.
--drop_genotype_annotation -DGA	string multiple	Genotype (`FORMAT`) annotations to drop from the output VCF, specified by their key. Can be specified multiple times.
--drop_info_annotation -DA	string multiple	`INFO` annotations to drop from the output VCF, specified by their key. Can be specified multiple times.
--exclude_filtered	boolean_true	Don't include filtered sites in the output VCF.
--exclude_ids -xl-ids	string multiple	List of variant rsIDs to exclude. Can be specified multiple times.
--exclude_intervals -XL	file	One or more genomic intervals to exclude from processing, provided as a file (e.g. BED, interval_list).
--exclude_non_variants	boolean_true	Don't include non-variant sites in the output VCF.
--exclude_sample_expressions -xl-se	string multiple	Regular expression(s) matching sample names to exclude. Can be specified multiple times.
--exclude_sample_name -xl-sn	string multiple	Exclude genotypes from this sample. Can be specified multiple times.
--ignore_non_ref_in_types	boolean_true	Ignore `NON_REF` alleles when determining variant type. Required for filtering GVCF files by type.
--intervals -L	file	One or more genomic intervals over which to operate, provided as a file (e.g. BED, interval_list).
--invert_mendelian_violation	boolean_true	Output non-Mendelian-violation sites only.
--invert_select -invert-select	boolean_true	Invert the selection criteria specified by `--select_expressions`.
--keep_ids -ids	string multiple	List of variant rsIDs to select. Can be specified multiple times.
--keep_original_ac	boolean_true	Store the original `AC`, `AF`, and `AN` values after subsetting.
--keep_original_dp	boolean_true	Store the original `DP` value after subsetting.
--max_filtered_genotypes	integer	Maximum number of samples filtered at the genotype level.
--max_fraction_filtered_genotypes	double	Maximum fraction of samples filtered at the genotype level.
--max_indel_size	integer	Maximum size of indels to include.
--max_nocall_fraction	double	Maximum fraction of samples with no-call genotypes.
--max_nocall_number	integer	Maximum number of samples with no-call genotypes.
--mendelian_violation	boolean_true	Output Mendelian violation sites only.
--mendelian_violation_qual_threshold	double	Minimum GQ score for each trio member to accept a site as a Mendelian violation.
--min_filtered_genotypes	integer	Minimum number of samples filtered at the genotype level.
--min_fraction_filtered_genotypes	double	Minimum fraction of samples filtered at the genotype level.
--min_indel_size	integer	Minimum size of indels to include.
--pedigree -ped	file	Pedigree file, used for pedigree-based analyses such as Mendelian violation detection (`--mendelian_violation`, `--invert_mendelian_violation`).
--preserve_alleles	boolean_true	Preserve original alleles, do not trim.
--remove_fraction_genotypes	double	Select a fraction of genotypes at random from the input and set them to no-call.
--remove_unused_alternates	boolean_true	Remove alternate alleles not present in any genotypes.
--restrict_alleles_to	string	Select only variants of a particular allelicity.
--sample_expressions -se	string multiple	Regular expression to select multiple samples. Can be specified multiple times.
--sample_name -sn	string multiple	Include genotypes from this sample. Can be specified multiple times.
--select_expressions --select	string multiple	A filtering expression in terms of either `INFO` fields or the `VariantContext` object (JEXL syntax). If the expression evaluates to `true` for a variant, it will be kept in the output VCF. Can be specified multiple times.
--select_genotype_expressions -select-genotype	string multiple	A filtering expression in terms of `FORMAT` fields. If the expression evaluates to `true` for a variant, it will be kept in the output VCF. Can be specified multiple times.
--select_random_fraction -fraction	double	Select a fraction of variants at random from the input.
--select_type_to_exclude -xl-select-type	string multiple	Do not select certain type of variants from the input file. Can be specified multiple times.
--select_type_to_include -select-type	string multiple	Select only a certain type of variants from the input file. Can be specified multiple times.
--set_filtered_gt_to_nocall	boolean_true	Set filtered genotypes to no-call.

Name

Type & Properties

--apply_jexl_filters_first

-jexl-first

boolean_true

--call_genotypes

boolean_true

--concordance

-conc

file

--discordance

-disc

file

--drop_genotype_annotation

-DGA

string

multiple

--drop_info_annotation

-DA

string

multiple

--exclude_filtered

boolean_true

--exclude_ids

-xl-ids

string

multiple

--exclude_intervals

-XL

file

--exclude_non_variants

boolean_true

--exclude_sample_expressions

-xl-se

string

multiple

--exclude_sample_name

-xl-sn

string

multiple

--ignore_non_ref_in_types

boolean_true

--intervals

-L

file

--invert_mendelian_violation

boolean_true

--invert_select

-invert-select

boolean_true

--keep_ids

-ids

string

multiple

--keep_original_ac

boolean_true

--keep_original_dp

boolean_true

--max_filtered_genotypes

integer

--max_fraction_filtered_genotypes

double

--max_indel_size

integer

--max_nocall_fraction

double

--max_nocall_number

integer

--mendelian_violation

boolean_true

--mendelian_violation_qual_threshold

double

--min_filtered_genotypes

integer

--min_fraction_filtered_genotypes

double

--min_indel_size

integer

--pedigree

-ped

file

--preserve_alleles

boolean_true

--remove_fraction_genotypes

double

--remove_unused_alternates

boolean_true

--restrict_alleles_to

string

--sample_expressions

-se

string

multiple

--sample_name

-sn

string

multiple

--select_expressions

--select

string

multiple

--select_genotype_expressions

-select-genotype

string

multiple

--select_random_fraction

-fraction

double

--select_type_to_exclude

-xl-select-type

string

multiple

--select_type_to_include

-select-type

string

multiple

--set_filtered_gt_to_nocall

boolean_true