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.gzWhen 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}, {@link FragmentLengthFilter}, 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
GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.
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