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 -- https://en.wikipedia.org/wiki/NUMT). For the value, provide the median coverage expected in autosomal regions with coverage.
USAGE: FilterMutectCalls [arguments]
Filter somatic SNVs and indels called by Mutect2
Version:4.1.7.0
Required Arguments:
--output,-O:String The output filtered VCF file Required.
--reference,-R:GATKPathSpecifier
Reference sequence file Required.
--variant,-V:String A VCF file containing variants Required.
Optional Arguments:
--add-output-sam-program-record,-add-output-sam-program-record:Boolean
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--arguments_file:File read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB:Integer
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB:Integer
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--contamination-estimate:Double
Estimate of contamination. Default value: 0.0.
--contamination-table:File Tables containing contamination information. This argument may be specified 0 or more
times. Default value: null.
--create-output-bam-index,-OBI:Boolean
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM:Boolean
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI:Boolean
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM:Boolean
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC:Boolean
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. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF:String
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible Values: {WellformedReadFilter}
--disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--distance-on-haplotype:Integer
On second filtering pass, variants with same PGT and PID tags as a filtered variant within
this distance are filtered. Default value: 100.
--exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--f-score-beta:Double F score beta, the relative weight of recall to precision, used if OPTIMAL_F_SCORE strategy
is chosen Default value: 1.0.
--false-discovery-rate:Double Maximum false discovery rate allowed if FALSE_DISCOVERY_RATE threshold strategy is chosen
Default value: 0.05.
--filtering-stats:String The output filtering stats file Default value: null.
--gatk-config-file:String A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries:Integer
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays:String
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. Default value: .
--help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
--initial-threshold:Double Initial artifact probability threshold used in first iteration Default value: 0.1.
--input,-I:String BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp:Integer
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr:IntervalMergingRule
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr:IntervalSetRule
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L:String One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false}
--log-artifact-prior:Double Initial ln prior probability that a called site is not a technical artifact Default
value: -2.302585092994046.
--log-indel-prior:Double Initial ln prior probability that a site has a somatic indel Default value:
-16.11809565095832.
--log-snv-prior:Double Initial ln prior probability that a site has a somatic SNV Default value:
-13.815510557964275.
--long-indel-length:Integer Indels of this length or greater are treated specially by the mapping quality filter.
Default value: 5.
--max-alt-allele-count:IntegerMaximum alt alleles per site. Default value: 1.
--max-events-in-region:IntegerMaximum events in a single assembly region. Filter all variants if exceeded. Default
value: 2.
--max-median-fragment-length-difference:Integer
Maximum difference between median alt and ref fragment lengths Default value: 10000.
--max-n-ratio:Double Maximum fraction of non-ref bases in the pileup that are N (unknown) Default value:
Infinity.
--min-allele-fraction:Double Minimum allele fraction required Default value: 0.0.
--min-median-base-quality:Integer
Minimum median base quality of alt reads Default value: 20.
--min-median-mapping-quality:Integer
Minimum median mapping quality of alt reads Default value: 30.
--min-median-read-position:Integer
Minimum median distance of variants from the end of reads Default value: 1.
--min-reads-per-strand:IntegerMinimum alt reads required on both forward and reverse strands Default value: 0.
--min-slippage-length:Integer Minimum number of reference bases in an STR to suspect polymerase slippage Default value:
8.
--mitochondria-mode:Boolean Set filters to mitochondrial defaults Default value: false. Possible values: {true,
false}
--normal-p-value-threshold:Double
P value threshold for normal artifact filter Default value: 0.001.
--orientation-bias-artifact-priors,-ob-priors:File
One or more .tar.gz files containing tables of prior artifact probabilities for the read
orientation filter model, one table per tumor sample This argument may be specified 0 or
more times. Default value: null.
--pcr-slippage-rate:Double The frequency of polymerase slippage in contexts where it is suspected Default value:
0.1.
--QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF:String Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter,
HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter,
ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter,
ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter,
SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter,
WellformedReadFilter}
--read-index,-read-index:String
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. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS:ValidationStringency
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. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--seconds-between-progress-updates,-seconds-between-progress-updates:Double
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary,-sequence-dictionary:String
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output:Boolean
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--stats:String The Mutect stats file output by Mutect2 Default value: null.
--threshold-strategy:Strategy The method for optimizing the posterior probability threshold Default value:
OPTIMAL_F_SCORE. Possible values: {CONSTANT, FALSE_DISCOVERY_RATE, OPTIMAL_F_SCORE}
--tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.
--tumor-segmentation:File Tables containing tumor segments' minor allele fractions for germline hets emitted by
CalculateContamination This argument may be specified 0 or more times. Default value:
null.
--unique-alt-read-count,-unique:Integer
Minimum unique (i.e. deduplicated) reads supporting the alternate allele Default value:
0.
--use-jdk-deflater,-jdk-deflater:Boolean
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater:Boolean
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity,-verbosity:LogLevel
Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version:Boolean display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--showHidden,-showHidden:Boolean
display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases:Integer Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjuction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac:Double Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction
with argument(s) maxAmbiguousBases
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length:Integer Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length:Integer Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals:String One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "LibraryReadFilter" is specified:
--library,-library:String Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality:Integer
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality:Integer
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length:Integer
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends:Boolean
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short:Integer Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name:String Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes:String Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list:StringA read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group:String The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length:Integer Keep only reads with length at most equal to the specified value Required.
--min-read-length:Integer Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name:String Keep only reads with this read name Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only:Boolean
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "SampleReadFilter" is specified:
--sample,-sample:String The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--invert-soft-clip-ratio-filter:Boolean
Inverts the results from this filter, causing all variants that would pass to fail and
visa-versa. Default value: false. Possible values: {true, false}
--soft-clipped-leading-trailing-ratio:Double
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjuction with
argument(s) minimumSoftClippedRatio
--soft-clipped-ratio-threshold:Double
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjuction with
argument(s) minimumLeadingTrailingSoftClippedRatio