Filter variant calls based on INFO and/or FORMAT annotations
Category Variant Filtering
Overview
Filter variant calls based on INFO and/or FORMAT annotationsThis 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.
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by VariantFiltration.
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.
--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
GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.
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