Select a subset of variants from a VCF file

Category Variant Manipulation

---

Overview

Select a subset of variants from a VCF file

This tool makes it possible to select a subset of variants based on various criteria in order to facilitate certain analyses. Examples of such analyses 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.

There are many different options for selecting subsets of variants from a larger callset:

• Extract one or more samples from a callset based on either a complete sample name or a pattern match.
• Specify criteria for inclusion that place thresholds on annotation values, e.g. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These criteria are written as "JEXL expressions", which are documented in the article about using JEXL expressions.
• Provide concordance or discordance tracks in order to include or exclude variants that are also present in other given callsets.
• Select variants based on criteria like their type (e.g. INDELs only), evidence of mendelian violation, filtering status, allelicity, etc.

There are also several options for recording the original values of certain annotations which are recalculated when one subsets the new callset, trims alleles, etc.

Input

A variant call set in VCF format from which a subset can be selected.

Output

A new VCF file containing the selected subset of variants.

*

Usage examples

Select SNPs

     gatk SelectVariants \
     -R Homo_sapiens_assembly38.fasta \
     -V input.vcf \
     --select-type-to-include SNP \
     -O output.vcf
 

Query Chromosome 20 Variants from a GenomicsDB

     gatk SelectVariants \
     -R Homo_sapiens_assembly38.fasta \
     -V gendb://genomicsDB \
     -L 20 \
     -O output.chr20.vcf
 

SelectVariants specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Required Arguments
--output  -O	null	File to which variants should be written
--variant  -V	null	A VCF file containing variants
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer  -CIPB	-1	Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloud-prefetch-buffer  -CPB	40	Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--concordance  -conc	null	Output variants also called in this comparison track
--disable-bam-index-caching  -DBIC	false	If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
--discordance  -disc	null	Output variants not called in this comparison track
--exclude-filtered	false	Don't include filtered sites
--exclude-ids  -xl-ids	[]	List of variant rsIDs to exclude
--exclude-non-variants	false	Don't include non-variant sites
--exclude-sample-expressions  -xl-se	[]	List of sample expressions to exclude
--exclude-sample-name  -xl-sn	[]	Exclude genotypes from this sample
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--help  -h	false	display the help message
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L	[]	One or more genomic intervals over which to operate
--invert-mendelian-violation	false	Output non-mendelian violation sites only
--invertSelect  -invert-select	false	Invert the selection criteria for -select
--keep-ids  -ids	[]	List of variant rsIDs to select
--keep-original-ac	false	Store the original AC, AF, and AN values after subsetting
--keep-original-dp	false	Store the original DP value after subsetting
--max-filtered-genotypes	2147483647	Maximum number of samples filtered at the genotype level
--max-fraction-filtered-genotypes	1.0	Maximum fraction of samples filtered at the genotype level
--max-indel-size	2147483647	Maximum size of indels to include
--max-nocall-fraction	1.0	Maximum fraction of samples with no-call genotypes
--max-nocall-number	2147483647	Maximum number of samples with no-call genotypes
--mendelian-violation	false	Output mendelian violation sites only
--mendelian-violation-qual-threshold	0.0	Minimum GQ score for each trio member to accept a site as a violation
--min-filtered-genotypes	0	Minimum number of samples filtered at the genotype level
--min-fraction-filtered-genotypes	0.0	Maximum fraction of samples filtered at the genotype level
--min-indel-size	0	Minimum size of indels to include
--pedigree  -ped	null	Pedigree file
--preserve-alleles	false	Preserve original alleles, do not trim
--reference  -R	null	Reference sequence
--remove-fraction-genotypes	0.0	Select a fraction of genotypes at random from the input and sets them to no-call
--remove-unused-alternates	false	Remove alternate alleles not present in any genotypes
--restrict-alleles-to	ALL	Select only variants of a particular allelicity
--sample-expressions  -se	[]	Regular expression to select multiple samples
--sample-name  -sn	[]	Include genotypes from this sample
--select-random-fraction  -fraction	0.0	Select a fraction of variants at random from the input
--select-type-to-exclude  -xl-select-type	[]	Do not select certain type of variants from the input file
--select-type-to-include  -select-type	[]	Select only a certain type of variants from the input file
--selectExpressions  -select	[]	One or more criteria to use when selecting the data
--set-filtered-gt-to-nocall	false	Set filtered genotypes to no-call
--version	false	display the version number for this tool
Optional Common Arguments
--add-output-sam-program-record	true	If true, adds a PG tag to created SAM/BAM/CRAM files.
--add-output-vcf-command-line	true	If true, adds a command line header line to created VCF files.
--create-output-bam-index  -OBI	true	If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5  -OBM	false	If true, create a MD5 digest for any BAM/SAM/CRAM file created
--create-output-variant-index  -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5  -OVM	false	If true, create a a MD5 digest any VCF file created.
--disable-read-filter  -DF	[]	Read filters to be disabled before analysis
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--disable-tool-default-read-filters	false	Disable all tool default read filters
--exclude-intervals  -XL	[]	One or more genomic intervals to exclude from processing
--gatk-config-file	null	A configuration file to use with the GATK.
--input  -I	[]	BAM/SAM/CRAM file containing reads
--interval-exclusion-padding  -ixp	0	Amount of padding (in bp) to add to each interval you are excluding.
--interval-padding  -ip	0	Amount of padding (in bp) to add to each interval you are including.
--interval-set-rule  -isr	UNION	Set merging approach to use for combining interval inputs
--lenient  -LE	false	Lenient processing of VCF files
--QUIET	false	Whether to suppress job-summary info on System.err.
--read-filter  -RF	[]	Read filters to be applied before analysis
--read-index	[]	Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
--read-validation-stringency  -VS	SILENT	Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--seconds-between-progress-updates	10.0	Output traversal statistics every time this many seconds elapse
--sequence-dictionary	null	Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--TMP_DIR	[]	Undocumented option
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

---

--add-output-sam-program-record / -add-output-sam-program-record

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true

---

--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean  true

---

--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []

---

--cloud-index-prefetch-buffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]

---

--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]

---

--concordance / -conc

Output variants also called in this comparison track
A site is considered concordant if (1) we are not looking for specific samples and there is a variant called in both the variant and concordance tracks or (2) every sample present in the variant track is present in the concordance track and they have the sample genotype call.

FeatureInput[VariantContext]  null

---

--create-output-bam-index / -OBI

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean  true

---

--create-output-bam-md5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false

---

--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

---

--create-output-variant-md5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean  false

---

--disable-bam-index-caching / -DBIC

If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.

boolean  false

---

--disable-read-filter / -DF

Read filters to be disabled before analysis

List[String]  []

---

--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation

If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!

boolean  false

---

--disable-tool-default-read-filters / -disable-tool-default-read-filters

Disable all tool default read filters

boolean  false

---

--discordance / -disc

Output variants not called in this comparison track
A site is considered discordant if there exists some sample in the variant track that has a non-reference genotype and either the site isn't present in this track, the sample isn't present in this track, or the sample is called reference in this track.

FeatureInput[VariantContext]  null

---

--exclude-filtered / NA

Don't include filtered sites
If this flag is enabled, sites that have been marked as filtered (i.e. have anything other than `.` or `PASS` in the FILTER field) will be excluded from the output.

boolean  false

---

--exclude-ids / -xl-ids

List of variant rsIDs to exclude
List of IDs (or a .list file containing ids) to exclude. The tool will exclude variants whose ID field is present in this list of IDs. The matching is done by exact string matching. If a file, the file name must end in ".list", and the expected file format is simply plain text with one ID per line.

Set[String]  []

---

--exclude-intervals / -XL

One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals).

List[String]  []

---

--exclude-non-variants / NA

Don't include non-variant sites

boolean  false

---

--exclude-sample-expressions / -xl-se

List of sample expressions to exclude
Using a regular expression allows you to match multiple sample names that have that pattern in common. Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded. This argument can be specified multiple times in order to use multiple different matching patterns.

Set[String]  []

---

--exclude-sample-name / -xl-sn

Exclude genotypes from this sample
Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded. This argument can be specified multiple times in order to provide multiple sample names, or to specify the name of one or more files containing sample names. File names must use the extension ".args", and the expected file format is simply plain text with one sample name per line.

Set[String]  []

---

--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

---

--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

---

--help / -h

display the help message

boolean  false

---

--input / -I

BAM/SAM/CRAM file containing reads

List[String]  []

---

--interval-exclusion-padding / -ixp

Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

---

--interval-merging-rule / -imr

Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:

ALL

OVERLAPPING_ONLY

IntervalMergingRule  ALL

---

--interval-padding / -ip

Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

---

--interval-set-rule / -isr

Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:

UNION

Take the union of all intervals

INTERSECTION

Take the intersection of intervals (the subset that overlaps all intervals specified)

IntervalSetRule  UNION

---

--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

---

--invert-mendelian-violation / NA

Output non-mendelian violation sites only
If this flag is enabled, this tool will select only variants that do not correspond to a mendelian violation as determined on the basis of family structure. Requires passing a pedigree file using the engine-level `-ped` argument.

Boolean  false

---

--invertSelect / -invert-select

Invert the selection criteria for -select
Invert the selection criteria for -select.

boolean  false

---

--keep-ids / -ids

List of variant rsIDs to select
List of IDs (or a .list file containing ids) to select. The tool will only select variants whose ID field is present in this list of IDs. The matching is done by exact string matching. If a file, the file name must end in ".list", and the expected file format is simply plain text with one ID per line.

Set[String]  []

---

--keep-original-ac / NA

Store the original AC, AF, and AN values after subsetting
When subsetting a callset, this tool recalculates the AC, AF, and AN values corresponding to the contents of the subset. If this flag is enabled, the original values of those annotations will be stored in new annotations called AC_Orig, AF_Orig, and AN_Orig.

boolean  false

---

--keep-original-dp / NA

Store the original DP value after subsetting
When subsetting a callset, this tool recalculates the site-level (INFO field) DP value corresponding to the contents of the subset. If this flag is enabled, the original value of the DP annotation will be stored in a new annotation called DP_Orig.

boolean  false

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

---

--max-filtered-genotypes / NA

Maximum number of samples filtered at the genotype level
If this argument is provided, select sites where at most a maximum number of samples are filtered at the genotype level.

int  2147483647  [ [ -∞  ∞ ] ]

---

--max-fraction-filtered-genotypes / NA

Maximum fraction of samples filtered at the genotype level
If this argument is provided, select sites where a fraction or less of the samples are filtered at the genotype level.

double  1.0  [ [ -∞  ∞ ] ]

---

--max-indel-size / NA

Maximum size of indels to include
If this argument is provided, indels that are larger than the specified size will be excluded.

int  2147483647  [ [ -∞  ∞ ] ]

---

--max-nocall-fraction / NA

Maximum fraction of samples with no-call genotypes
If this argument is provided, select sites where at most the given fraction of samples have no-call genotypes.

double  1.0  [ [ -∞  ∞ ] ]

---

--max-nocall-number / NA

Maximum number of samples with no-call genotypes
If this argument is provided, select sites where at most the given number of samples have no-call genotypes.

int  2147483647  [ [ -∞  ∞ ] ]

---

--mendelian-violation / NA

Output mendelian violation sites only
If this flag is enabled, this tool will select only variants that correspond to a mendelian violation as determined on the basis of family structure. Requires passing a pedigree file using the engine-level `-ped` argument.

Boolean  false

---

--mendelian-violation-qual-threshold / NA

Minimum GQ score for each trio member to accept a site as a violation
This argument specifies the genotype quality (GQ) threshold that all members of a trio must have in order for a site to be accepted as a mendelian violation. Note that the `-mv` flag must be set for this argument to have an effect.

double  0.0  [ [ -∞  ∞ ] ]

---

--min-filtered-genotypes / NA

Minimum number of samples filtered at the genotype level
If this argument is provided, select sites where at least a minimum number of samples are filtered at the genotype level.

int  0  [ [ -∞  ∞ ] ]

---

--min-fraction-filtered-genotypes / NA

Maximum fraction of samples filtered at the genotype level
If this argument is provided, select sites where a fraction or more of the samples are filtered at the genotype level.

double  0.0  [ [ -∞  ∞ ] ]

---

--min-indel-size / NA

Minimum size of indels to include
If this argument is provided, indels that are smaller than the specified size will be excluded.

int  0  [ [ -∞  ∞ ] ]

---

--output / -O

File to which variants should be written

R File  null

---

--pedigree / -ped

Pedigree file

File  null

---

--preserve-alleles / NA

Preserve original alleles, do not trim
The default behavior of this tool is to remove bases common to all remaining alleles after subsetting operations have been completed, leaving only their minimal representation. If this flag is enabled, the original alleles will be preserved as recorded in the input VCF.

boolean  false

---

--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false

---

--read-filter / -RF

Read filters to be applied before analysis

List[String]  []

---

--read-index / -read-index

Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.

List[String]  []

---

--read-validation-stringency / -VS

Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT

LENIENT

SILENT

ValidationStringency  SILENT

---

--reference / -R

Reference sequence

String  null

---

--remove-fraction-genotypes / NA

Select a fraction of genotypes at random from the input and sets them to no-call
The value of this argument should be a number between 0 and 1 specifying the fraction of total variants to be randomly selected from the input callset and set to no-call (./). Note that this is done using a probabilistic function, so the final result is not guaranteed to carry the exact fraction requested. Can be used for large fractions.

double  0.0  [ [ -∞  ∞ ] ]

---

--remove-unused-alternates / NA

Remove alternate alleles not present in any genotypes
When this flag is enabled, all alternate alleles that are not present in the (output) samples will be removed. Note that this even extends to biallelic SNPs - if the alternate allele is not present in any sample, it will be removed and the record will contain a '.' in the ALT column. Note also that sites-only VCFs, by definition, do not include the alternate allele in any genotype calls.

boolean  false

---

--restrict-alleles-to / NA

Select only variants of a particular allelicity
When this argument is used, we can choose to include only multiallelic or biallelic sites, depending on how many alleles are listed in the ALT column of a VCF. For example, a multiallelic record such as: 1 100 . A AAA,AAAAA will be excluded if `-restrict-alleles-to BIALLELIC` is used, because there are two alternate alleles, whereas a record such as: 1 100 . A T will be included in that case, but would be excluded if `-restrict-alleles-to MULTIALLELIC` is used. Valid options are ALL (default), MULTIALLELIC or BIALLELIC.

The --restrict-alleles-to argument is an enumerated type (NumberAlleleRestriction), which can have one of the following values:

ALL

BIALLELIC

MULTIALLELIC

NumberAlleleRestriction  ALL

---

--sample-expressions / -se

Regular expression to select multiple samples
Using a regular expression allows you to match multiple sample names that have that pattern in common. This argument can be specified multiple times in order to use multiple different matching patterns.

Set[String]  []

---

--sample-name / -sn

Include genotypes from this sample
This argument can be specified multiple times in order to provide multiple sample names, or to specify the name of one or more files containing sample names. File names must use the extension ".args", and the expected file format is simply plain text with one sample name per line. Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.

Set[String]  []

---

--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

---

--select-random-fraction / -fraction

Select a fraction of variants at random from the input
The value of this argument should be a number between 0 and 1 specifying the fraction of total variants to be randomly selected from the input callset. Note that this is done using a probabilistic function, so the final result is not guaranteed to carry the exact fraction requested. Can be used for large fractions.

double  0.0  [ [ -∞  ∞ ] ]

---

--select-type-to-exclude / -xl-select-type

Do not select certain type of variants from the input file
This argument excludes particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times.

List[Type]  []

---

--select-type-to-include / -select-type

Select only a certain type of variants from the input file
This argument selects particular kinds of variants out of a list. If left empty, there is no type selection and all variant types are considered for other selection criteria. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times.

List[Type]  []

---

--selectExpressions / -select

One or more criteria to use when selecting the data
See example commands above for detailed usage examples. Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.

ArrayList[String]  []

---

--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

String  null

---

--set-filtered-gt-to-nocall / NA

Set filtered genotypes to no-call
If this argument is provided, set filtered genotypes to no-call (./.).

boolean  false

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--TMP_DIR / NA

Undocumented option

List[File]  []

---

--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

---

--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

---

--variant / -V

A VCF file containing variants

R String  null

---

--verbosity / -verbosity

Control verbosity of logging.

The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

---

--version / NA

display the version number for this tool

boolean  false

---

Return to top

---

GATK version 4.0.1.2 built at 02-02-2019 02:02:55.