Filter variant calls based on INFO and/or FORMAT annotations

Category Variant Filtering

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Overview

Filter variant calls based on INFO and/or FORMAT annotations

This tool is designed for hard-filtering variant calls based on certain criteria. Records are hard-filtered by changing the value in the FILTER field to something other than PASS. Filtered records will be preserved in the output unless their removal is requested in the command line.

Inputs

• A VCF of variant calls to filter.
• One or more filtering expressions and corresponding filter names.

Output

A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed.

Usage example

   gatk VariantFiltration \
   -R reference.fasta \
   -V input.vcf.gz \
   -O output.vcf.gz \
   --filter-name "my_filter1" \
   --filter-expression "AB < 0.2" \
   --filter-name "my_filter2" \
   --filter-expression "MQ0 > 50"
 

Note

Composing filtering expressions can range from very simple to extremely complicated depending on what you're trying to do.

Compound expressions (ones that specify multiple conditions connected by &&, AND, ||, or OR, and reference multiple attributes) require special consideration. By default, variants that are missing one or more of the attributes referenced in a compound expression are treated as PASS for the entire expression, even if the variant would satisfy the filter criteria for another part of the expression. This can lead to unexpected results if any of the attributes referenced in a compound expression are present for some variants, but missing for others.

It is strongly recommended that such expressions be provided as individual arguments, each referencing a single attribute and specifying a single criteria. This ensures that all of the individual expression are applied to each variant, even if a given variant is missing values for some of the expression conditions.

As an example, multiple individual expressions provided like this:

   gatk VariantFiltration \
   -R reference.fasta \
   -V input.vcf.gz \
   -O output.vcf.gz \
   --filter-name "my_filter1" \
   --filter-expression "AB < 0.2" \
   --filter-name "my_filter2" \
   --filter-expression "MQ0 > 50"
 

are preferable to a single compound expression such as this:

    gatk VariantFiltration \
    -R reference.fasta \
    -V input.vcf.gz \
    -O output.vcf.gz \
    --filter-name "my_filter" \
    --filter-expression "AB < 0.2 || MQ0 > 50"
  

See this article about using JEXL expressions for more information.

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Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by VariantFiltration.

• WellformedReadFilter

VariantFiltration 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		File to which variants should be written
--variant  -V		A VCF file containing variants
Optional Tool Arguments
--apply-allele-specific-filters	false	Set mask at the allele level. This option is not compatible with clustering.
--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).
--cluster-size  -cluster	3	The number of SNPs which make up a cluster. Must be at least 2
--cluster-window-size  -window	0	The window size (in bases) in which to evaluate clustered SNPs
--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.
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--filter-expression  -filter		One or more expressions used with INFO fields to filter
--filter-name		Names to use for the list of filters
--filter-not-in-mask	false	Filter records NOT in given input mask.
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays		Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
--genotype-filter-expression  -G-filter		One or more expressions used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)
--genotype-filter-name  -G-filter-name		Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
--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
--invalidate-previous-filters	false	Remove previous filters applied to the VCF
--invert-filter-expression  -invfilter	false	Invert the selection criteria for --filter-expression
--invert-genotype-filter-expression  -invG-filter	false	Invert the selection criteria for --genotype-filter-expression
--mask		Input mask
--mask-extension	0	How many bases beyond records from a provided 'mask' should variants be filtered
--mask-name	Mask	The text to put in the FILTER field if a 'mask' is provided and overlaps with a variant call
--missing-values-evaluate-as-failing	false	When evaluating the JEXL expressions, missing values should be considered failing the expression
--reference  -R		Reference sequence
--set-filtered-genotype-to-no-call	false	Set filtered genotypes to no-call
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--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-tool-default-read-filters	false	Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
--exclude-intervals  -XL		One or more genomic intervals to exclude from processing
--gatk-config-file		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
--max-variants-per-shard	0	If non-zero, partitions VCF output into shards, each containing up to the given number of records.
--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		Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--tmp-dir		Temp directory to use.
--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.

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--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

---

--apply-allele-specific-filters

Set mask at the allele level. This option is not compatible with clustering.

boolean  false

---

--arguments_file

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  [ [ -∞  ∞ ] ]

---

--cluster-size / -cluster

The number of SNPs which make up a cluster. Must be at least 2
Works together with the --cluster-window-size argument.

Integer  3  [ [ -∞  ∞ ] ]

---

--cluster-window-size / -window

The window size (in bases) in which to evaluate clustered SNPs
Works together with the --cluster-size argument. To disable the clustered SNP filter, set this value to less than 1.

Integer  0  [ [ -∞  ∞ ] ]

---

--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 (WARNING: many tools will not function correctly without their default read filters on)

boolean  false

---

--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]  []

---

--filter-expression / -filter

One or more expressions used with INFO fields to filter
VariantFiltration accepts any number of JEXL expressions (so you can have two named filters by using --filter-name One --filter-expression "X < 1" --filter-name Two --filter-expression "X > 2"). It is preferable to use multiple expressions, each specifying an individual filter criteria, to a single compound expression that specifies multiple filter criteria.

List[String]  []

---

--filter-name

Names to use for the list of filters
This name is put in the FILTER field for variants that get filtered. Note that there must be a 1-to-1 mapping between filter expressions and filter names.

List[String]  []

---

--filter-not-in-mask

Filter records NOT in given input mask.
By default, if the --mask argument is used, any variant falling in a mask will be filtered. If this argument is used, logic is reversed, and variants falling outside a given mask will be filtered. Use case is, for example, if we have an interval list or BED file with "good" sites. Note that it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).

boolean  false

---

--gatk-config-file

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  [ [ -∞  ∞ ] ]

---

--gcs-project-for-requester-pays

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String  ""

---

--genotype-filter-expression / -G-filter

One or more expressions used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead. VariantFiltration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag). One can filter normally based on most fields (e.g. "GQ < 5.0"), but the GT (genotype) field is an exception. We have put in convenience methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1"). Also available are expressions isCalled, isNoCall, isMixed, and isAvailable, in accordance with the methods of the Genotype object. It is preferable to use multiple expressions, each specifying an individual filter criteria, to a single compound expression that specifies multiple filter criteria.

List[String]  []

---

--genotype-filter-name / -G-filter-name

Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.

List[String]  []

---

--help / -h

display the help message

boolean  false

---

--input / -I

BAM/SAM/CRAM file containing reads

List[GATKPath]  []

---

--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]  []

---

--invalidate-previous-filters

Remove previous filters applied to the VCF
Invalidate previous filters applied to the VariantContext, applying only the filters here

boolean  false

---

--invert-filter-expression / -invfilter

Invert the selection criteria for --filter-expression
Invert the selection criteria for --filter-expression

boolean  false

---

--invert-genotype-filter-expression / -invG-filter

Invert the selection criteria for --genotype-filter-expression
Invert the selection criteria for --genotype-filter-expression

boolean  false

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

---

--mask / -mask

Input mask
Any variant which overlaps entries from the provided mask file will be filtered. If the user wants logic to be reversed, i.e. filter variants that do not overlap with provided mask, then argument --filter-not-in-mask can be used. Note that it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).

FeatureInput[Feature]  null

---

--mask-extension

How many bases beyond records from a provided 'mask' should variants be filtered

Integer  0  [ [ -∞  ∞ ] ]

---

--mask-name

The text to put in the FILTER field if a 'mask' is provided and overlaps with a variant call
When using the --mask argument, the mask-name will be annotated in the variant record. Note that when using the --filter-not-in-mask argument to reverse the masking logic, it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).

String  Mask

---

--max-variants-per-shard

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int  0  [ [ 0  ∞ ] ]

---

--missing-values-evaluate-as-failing

When evaluating the JEXL expressions, missing values should be considered failing the expression
By default, if JEXL cannot evaluate your expression for a particular record because one of the annotations is not present, the whole expression evaluates as PASSing. Use this argument to have it evaluate as failing filters instead for these cases.

Boolean  false

---

--output / -O

File to which variants should be written

R GATKPath  null

---

--QUIET

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[GATKPath]  []

---

--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

GATKPath  null

---

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

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

---

--sequence-dictionary / -sequence-dictionary

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

GATKPath  null

---

--set-filtered-genotype-to-no-call

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

---

--sites-only-vcf-output

If true, don't emit genotype fields when writing vcf file output.

boolean  false

---

--tmp-dir

Temp directory to use.

GATKPath  null

---

--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 GATKPath  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

display the version number for this tool

boolean  false

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GATK version 4.2.6.1-SNAPSHOT built at Wed, 13 Apr 2022 13:12:10 -0700.