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FilterMutectCalls

Filter somatic SNVs and indels called by Mutect2

Category Variant Filtering


Overview

Filter variants in a Mutect2 VCF callset.

FilterMutectCalls applies filters to the raw output of Mutect2. Parameters are contained in M2FiltersArgumentCollection and described in https://github.com/broadinstitute/gatk/tree/master/docs/mutect/mutect.pdf. To filter based on sequence context artifacts, specify the --orientation-bias-artifact-priors [artifact priors tar.gz file] argument one or more times. This input is generated by LearnReadOrientationModel.

If given a --contamination-table file, e.g. results from CalculateContamination, the tool will additionally filter variants due to contamination. This argument may be specified with a table for one or more tumor samples. Alternatively, provide an estimate of the contamination with the --contamination argument. FilterMutectCalls can also be given one or more --tumor-segmentation files, which are also output by CalculateContamination.

This tool is featured in the Somatic Short Mutation calling Best Practice Workflow. See Tutorial#11136 for a step-by-step description of the workflow and Article#11127 for an overview of what traditional somatic calling entails. For the latest pipeline scripts, see the Mutect2 WDL scripts directory.

Usage example

 gatk FilterMutectCalls \
   -R reference.fasta \
   -V somatic.vcf.gz \
   --contamination-table contamination.table \
   --tumor-segmentation segments.tsv \
   -O filtered.vcf.gz
 
When running on unfiltered output of Mutect2 in --mitochondria mode, setting the advanced option --autosomal-coverage argument (default 0) activates a recommended filter against likely erroneously mapped NuMTs (nuclear mitochondrial DNA segments). For the value, provide the median coverage expected in autosomal regions with coverage.

Additional Information

Read filters

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

FilterMutectCalls 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 The output filtered VCF file
--reference
 -R
null Reference sequence file
--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
--autosomal-coverage
0.0 Median autosomal coverage for filtering potential polymporphic NuMTs when calling on mitochondria.
--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).
--contamination-estimate
0.0 Estimate of contamination.
--contamination-table
[] Tables containing contamination information.
--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!
--distance-on-haplotype
100 On second filtering pass, variants with same PGT and PID tags as a filtered variant within this distance are filtered.
--f-score-beta
1.0 F score beta, the relative weight of recall to precision, used if OPTIMAL_F_SCORE strategy is chosen
--false-discovery-rate
0.05 Maximum false discovery rate allowed if FALSE_DISCOVERY_RATE threshold strategy is chosen
--filtering-stats
null The output filtering stats file
--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.
--help
 -h
false display the help message
--initial-threshold
0.1 Initial artifact probability threshold used in first iteration
--interval-merging-rule
 -imr
ALL Interval merging rule for abutting intervals
--intervals
 -L
[] One or more genomic intervals over which to operate
--log-artifact-prior
-2.302585092994046 Initial ln prior probability that a called site is not a technical artifact
--log-indel-prior
-16.11809565095832 Initial ln prior probability that a site has a somatic indel
--log-snv-prior
-13.815510557964275 Initial ln prior probability that a site has a somatic SNV
--long-indel-length
5 Indels of this length or greater are treated specially by the mapping quality filter.
--max-alt-allele-count
1 Maximum alt alleles per site.
--max-events-in-region
2 Maximum events in a single assembly region. Filter all variants if exceeded.
--max-median-fragment-length-difference
10000 Maximum difference between median alt and ref fragment lengths
--max-n-ratio
Infinity Maximum fraction of non-ref bases in the pileup that are N (unknown)
--max-numt-fraction
0.85 Maximum fraction of alt reads that originally aligned outside the mitochondria. These are due to NuMTs.
--min-allele-fraction
0.0 Minimum allele fraction required
--min-median-base-quality
20 Minimum median base quality of alt reads
--min-median-mapping-quality
30 Minimum median mapping quality of alt reads
--min-median-read-position
1 Minimum median distance of variants from the end of reads
--min-reads-per-strand
0 Minimum alt reads required on both forward and reverse strands
--min-slippage-length
8 Minimum number of reference bases in an STR to suspect polymerase slippage
--mitochondria-mode
false Set filters to mitochondrial defaults
--normal-p-value-threshold
0.001 P value threshold for normal artifact filter
--orientation-bias-artifact-priors
 -ob-priors
[] One or more .tar.gz files containing tables of prior artifact probabilities for the read orientation filter model, one table per tumor sample
--pcr-slippage-rate
0.1 The frequency of polymerase slippage in contexts where it is suspected
--sites-only-vcf-output
false If true, don't emit genotype fields when writing vcf file output.
--stats
null The Mutect stats file output by Mutect2
--threshold-strategy
OPTIMAL_F_SCORE The method for optimizing the posterior probability threshold
--tumor-segmentation
[] Tables containing tumor segments' minor allele fractions for germline hets emitted by CalculateContamination
--unique-alt-read-count
 -unique
0 Minimum unique (i.e. deduplicated) reads supporting the alternate allele
--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
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
null 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


--arguments_file / NA

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

List[File]  []


--autosomal-coverage / NA

Median autosomal coverage for filtering potential polymporphic NuMTs when calling on mitochondria.

double  0.0  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--contamination-estimate / NA

Estimate of contamination.

double  0.0  [ [ -∞  ∞ ] ]


--contamination-table / NA

Tables containing contamination information.

List[File]  []


--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


--distance-on-haplotype / NA

On second filtering pass, variants with same PGT and PID tags as a filtered variant within this distance are filtered.

int  100  [ [ -∞  ∞ ] ]


--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]  []


--f-score-beta / NA

F score beta, the relative weight of recall to precision, used if OPTIMAL_F_SCORE strategy is chosen

double  1.0  [ [ -∞  ∞ ] ]


--false-discovery-rate / NA

Maximum false discovery rate allowed if FALSE_DISCOVERY_RATE threshold strategy is chosen

double  0.05  [ [ -∞  ∞ ] ]


--filtering-stats / NA

The output filtering stats file

String  null


--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  [ [ -∞  ∞ ] ]


--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""


--help / -h

display the help message

boolean  false


--initial-threshold / NA

Initial artifact probability threshold used in first iteration

double  0.1  [ [ -∞  ∞ ] ]


--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]  []


--lenient / -LE

Lenient processing of VCF files

boolean  false


--log-artifact-prior / NA

Initial ln prior probability that a called site is not a technical artifact

double  -2.302585092994046  [ [ -∞  ∞ ] ]


--log-indel-prior / NA

Initial ln prior probability that a site has a somatic indel

double  -16.11809565095832  [ [ -∞  ∞ ] ]


--log-snv-prior / NA

Initial ln prior probability that a site has a somatic SNV

double  -13.815510557964275  [ [ -∞  ∞ ] ]


--long-indel-length / NA

Indels of this length or greater are treated specially by the mapping quality filter.

int  5  [ [ -∞  ∞ ] ]


--max-alt-allele-count / NA

Maximum alt alleles per site.

int  1  [ [ -∞  ∞ ] ]


--max-events-in-region / NA

Maximum events in a single assembly region. Filter all variants if exceeded.

int  2  [ [ -∞  ∞ ] ]


--max-median-fragment-length-difference / NA

Maximum difference between median alt and ref fragment lengths

int  10000  [ [ -∞  ∞ ] ]


--max-n-ratio / NA

Maximum fraction of non-ref bases in the pileup that are N (unknown)

double  Infinity  [ [ -∞  ∞ ] ]


--max-numt-fraction / NA

Maximum fraction of alt reads that originally aligned outside the mitochondria. These are due to NuMTs.

double  0.85  [ [ -∞  ∞ ] ]


--min-allele-fraction / NA

Minimum allele fraction required

double  0.0  [ [ -∞  ∞ ] ]


--min-median-base-quality / NA

Minimum median base quality of alt reads

int  20  [ [ -∞  ∞ ] ]


--min-median-mapping-quality / NA

Minimum median mapping quality of alt reads

int  30  [ [ -∞  ∞ ] ]


--min-median-read-position / NA

Minimum median distance of variants from the end of reads

int  1  [ [ -∞  ∞ ] ]


--min-reads-per-strand / NA

Minimum alt reads required on both forward and reverse strands

int  0  [ [ -∞  ∞ ] ]


--min-slippage-length / NA

Minimum number of reference bases in an STR to suspect polymerase slippage

int  8  [ [ -∞  ∞ ] ]


--mitochondria-mode / NA

Set filters to mitochondrial defaults
Mitochondria mode includes the filter{@link ChimericOriginalAlignmentFilter} and {@link PolymorphicNuMTFilter}, and excludes the filters {@link ClusteredEventsFilter}, {@link MultiallelicFilter}, {@link PolymeraseSlippageFilter}, {@link FilteredHaplotypeFilter}, and {@link GermlineFilter}

boolean  false


--normal-p-value-threshold / NA

P value threshold for normal artifact filter

double  0.001  [ [ -∞  ∞ ] ]


--orientation-bias-artifact-priors / -ob-priors

One or more .tar.gz files containing tables of prior artifact probabilities for the read orientation filter model, one table per tumor sample

List[File]  []


--output / -O

The output filtered VCF file

R String  null


--pcr-slippage-rate / NA

The frequency of polymerase slippage in contexts where it is suspected

double  0.1  [ [ -∞  ∞ ] ]


--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 file

R String  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.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--sites-only-vcf-output / NA

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

boolean  false


--stats / NA

The Mutect stats file output by Mutect2

String  null


--threshold-strategy / NA

The method for optimizing the posterior probability threshold

The --threshold-strategy argument is an enumerated type (Strategy), which can have one of the following values:

CONSTANT
FALSE_DISCOVERY_RATE
OPTIMAL_F_SCORE

Strategy  OPTIMAL_F_SCORE


--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  null


--tumor-segmentation / NA

Tables containing tumor segments' minor allele fractions for germline hets emitted by CalculateContamination

List[File]  []


--unique-alt-read-count / -unique

Minimum unique (i.e. deduplicated) reads supporting the alternate allele

int  0  [ [ -∞  ∞ ] ]


--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


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GATK version 4.1.3.0 built at Fri, 9 Aug 2019 21:16:03 -0400.