FilterMutectCalls – GATK

Filter somatic SNVs and indels called by Mutect2

Category Variant Filtering

Overview

Filter variants in a Mutect2 VCF callset.

FilterMutectCalls encapsulates GATK3 MuTect2's filtering functionality and adds additional filters. Thresholds for filters 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, see FilterByOrientationBias.

Filtering thresholds for both normal-artifact-lod (default threshold 0.0) and tumor-lod (default threshold 5.3) can be set in this tool. If the normal artifact log odds is larger than the threshold, then FilterMutectCalls applies the artifact-in-normal filter. For matched normal analyses with tumor contamination in the normal, consider increasing the normal-artifact-lod threshold. If the tumor log odds is smaller than the threshold, then FilterMutectCalls filters the variant.

If given a --contamination-table file, e.g. results from CalculateContamination, the tool will additionally filter on contamination fractions. Alternatively, provide a numerical fraction to filter with the --contamination argument.

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 \
   -V somatic.vcf.gz \
   --contamination-table contamination.table \
   -O filtered.vcf.gz

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
--variant -V	null	A VCF file containing variants
Optional Tool Arguments
--alleles	null	The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
--annotate-with-num-discovered-alleles	false	If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
--arguments_file	[]	read one or more arguments files and add them to the command line
--base-quality-score-threshold	18	Base qualities below this threshold will be reduced to the minimum (6)
--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-fraction-to-filter -contamination	0.0	Fraction of contamination in sequencing data (for all samples) to aggressively remove
--contamination-table	null	Table 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.
--gcs-max-retries -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--genotyping-mode	DISCOVERY	Specifies how to determine the alternate alleles to use for genotyping
--graph-output -graph	null	Write debug assembly graph information to this file
--help -h	false	display the help message
--heterozygosity	0.001	Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
--heterozygosity-stdev	0.01	Standard deviation of heterozygosity for SNP and indel calling.
--indel-heterozygosity	1.25E-4	Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
--interval-merging-rule -imr	ALL	Interval merging rule for abutting intervals
--intervals -L	[]	One or more genomic intervals over which to operate
--log-somatic-prior	-6.0	Prior probability that a given site has a somatic allele.
--max-alt-allele-count	1	filter variants with too many alt alleles
--max-contamination-probability	0.1	Filter variants with posterior probability to be due to contamination greater than this.
--max-events-in-region	2	Variants coming from an assembly region with more than this many events are filtered
--max-germline-posterior	0.1	Maximum posterior probability that an allele is a germline variant
--max-median-fragment-length-difference	10000	filter variants for which alt reads' median fragment length is very different from the median for ref reads.
--max-strand-artifact-probability -strand-prob	0.99	Filter a variant if the probability of strand artifact exceeds this number
--min-base-quality-score -mbq	10	Minimum base quality required to consider a base for calling
--min-median-base-quality	20	filter variants for which alt reads' median base quality is too low.
--min-median-mapping-quality	30	filter variants for which alt reads' median mapping quality is too low.
--min-median-read-position	5	filter variants for which the median position of alt alleles within reads is too near the end of reads.
--min-pcr-slippage-size	8	Minimum number of reference bases in an STR to suspect PCR slippage
--min-strand-artifact-allele-fraction -strand-af	0.01	Only filter a variant if the MAP estimate of allele fraction given artifact is below this number
--native-pair-hmm-threads	4	How many threads should a native pairHMM implementation use
--native-pair-hmm-use-double-precision	false	use double precision in the native pairHmm. This is slower but matches the java implementation better
--normal-artifact-lod	0.0	LOD threshold for calling normal artifacts
--normal-p-value-threshold	0.001	P value threshold for normal artifact filter
--num-reference-samples-if-no-call	0	Number of hom-ref genotypes to infer at sites not present in a panel
--orientation-bias-fdr	0.05	Mutect will calculate the threshold for the read orientation filter such that the FDR doesn't exceed this value
--output-mode	EMIT_VARIANTS_ONLY	Specifies which type of calls we should output
--pcr-slippage-p-value	0.001	P-value threshold for PCR slippage
--pcr-slippage-rate	0.1	In contexts where PCR slippage is suspected, the rough fraction of reads in which slippage occurs
--population-callset -population	null	Callset to use in calculating genotype priors
--reference -R	null	Reference sequence
--sample-ploidy -ploidy	2	Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--standard-min-confidence-threshold-for-calling -stand-call-conf	10.0	The minimum phred-scaled confidence threshold at which variants should be called
--stats	Mutect2FilteringStats.tsv	Write the filtering statistics to this file
--tumor-lod	5.3	LOD threshold for calling tumor variant
--tumor-segmentation	null	Pileup summaries for the tumor sample as output by CalculateContamination
--unique-alt-read-count -unique	0	Filter a variant if a site contains fewer than this many unique (i.e. deduplicated) reads supporting the alternate allele
--use-new-qual-calculator -new-qual	false	If provided, we will use the new AF model instead of the so-called exact model
--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	[]	Undocumented option
--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
--all-site-pls	false	Annotate all sites with PLs
--allow-non-unique-kmers-in-ref	false	Allow graphs that have non-unique kmers in the reference
--bam-output -bamout	null	File to which assembled haplotypes should be written
--bam-writer-type	CALLED_HAPLOTYPES	Which haplotypes should be written to the BAM
--consensus	false	1000G consensus mode
--contamination-fraction-per-sample-file -contamination-file	null	Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be "" (Contamination is double) per line; No header.
--debug	false	Print out very verbose debug information about each triggering active region
--do-not-run-physical-phasing	false	Disable physical phasing
--dont-increase-kmer-sizes-for-cycles	false	Disable iterating over kmer sizes when graph cycles are detected
--dont-trim-active-regions	false	If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping
--dont-use-soft-clipped-bases	false	Do not analyze soft clipped bases in the reads
--genotype-filtered-alleles	false	Whether to genotype all given alleles, even filtered ones, --genotyping_mode is GENOTYPE_GIVEN_ALLELES
--input-prior	[]	Input prior for calls
--kmer-size	[10, 25]	Kmer size to use in the read threading assembler
--max-alternate-alleles	6	Maximum number of alternate alleles to genotype
--max-genotype-count	1024	Maximum number of genotypes to consider at any site
--max-num-haplotypes-in-population	128	Maximum number of haplotypes to consider for your population
--min-dangling-branch-length	4	Minimum length of a dangling branch to attempt recovery
--min-pruning	2	Minimum support to not prune paths in the graph
--num-pruning-samples	1	Number of samples that must pass the minPruning threshold
--pair-hmm-gap-continuation-penalty	10	Flat gap continuation penalty for use in the Pair HMM
--pair-hmm-implementation -pairHMM	FASTEST_AVAILABLE	The PairHMM implementation to use for genotype likelihood calculations
--pcr-indel-model	CONSERVATIVE	The PCR indel model to use
--phred-scaled-global-read-mismapping-rate	45	The global assumed mismapping rate for reads
--showHidden	false	display hidden arguments
--smith-waterman	JAVA	Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice
--use-filtered-reads-for-annotations	false	Use the contamination-filtered read maps for the purposes of annotating variants
Deprecated Arguments
--recover-dangling-heads	false	This argument is deprecated since version 3.3

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

--all-site-pls / NA

Annotate all sites with PLs
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_SITES output mode is set, when we set this argument then we will also emit PLs at all sites. This will give a measure of reference confidence and a measure of which alt alleles are more plausible (if any). WARNINGS: - This feature will inflate VCF file size considerably. - All SNP ALT alleles will be emitted with corresponding 10 PL values. - An error will be emitted if EMIT_ALL_SITES is not set, or if anything other than diploid SNP model is used

boolean false

--alleles / NA

The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
When the caller is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding

FeatureInput[VariantContext] null

--allow-non-unique-kmers-in-ref / NA

Allow graphs that have non-unique kmers in the reference
By default, the program does not allow processing of reference sections that contain non-unique kmers. Disabling this check may cause problems in the assembly graph.

boolean false

--annotate-with-num-discovered-alleles / NA

If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping. Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.

boolean false

--arguments_file / NA

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

List[File] []

--bam-output / -bamout

File to which assembled haplotypes should be written
The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. Really for debugging purposes only. Note that the output here does not include uninformative reads so that not every input read is emitted to the bam. Turning on this mode may result in serious performance cost for the caller. It's really only appropriate to use in specific areas where you want to better understand why the caller is making specific calls. The reads are written out containing an "HC" tag (integer) that encodes which haplotype each read best matches according to the haplotype caller's likelihood calculation. The use of this tag is primarily intended to allow good coloring of reads in IGV. Simply go to "Color Alignments By > Tag" and enter "HC" to more easily see which reads go with these haplotype. Note that the haplotypes (called or all, depending on mode) are emitted as single reads covering the entire active region, coming from sample "HC" and a special read group called "ArtificialHaplotype". This will increase the pileup depth compared to what would be expected from the reads only, especially in complex regions. Note also that only reads that are actually informative about the haplotypes are emitted. By informative we mean that there's a meaningful difference in the likelihood of the read coming from one haplotype compared to its next best haplotype. If multiple BAMs are passed as input to the tool (as is common for M2), then they will be combined in the bamout output and tagged with the appropriate sample names. The best way to visualize the output of this mode is with IGV. Tell IGV to color the alignments by tag, and give it the "HC" tag, so you can see which reads support each haplotype. Finally, you can tell IGV to group by sample, which will separate the potential haplotypes from the reads. All of this can be seen in this screenshot

String null

--bam-writer-type / NA

Which haplotypes should be written to the BAM
The type of BAM output we want to see. This determines whether HC will write out all of the haplotypes it considered (top 128 max) or just the ones that were selected as alleles and assigned to samples.

The --bam-writer-type argument is an enumerated type (WriterType), which can have one of the following values:

ALL_POSSIBLE_HAPLOTYPES: A mode that's for method developers. Writes out all of the possible haplotypes considered, as well as reads aligned to each
CALLED_HAPLOTYPES: A mode for users. Writes out the reads aligned only to the called haplotypes. Useful to understand why the caller is calling what it is

WriterType CALLED_HAPLOTYPES

--base-quality-score-threshold / NA

Base qualities below this threshold will be reduced to the minimum (6)
Bases with a quality below this threshold will reduced to the minimum usable qualiy score (6).

byte 18 [ [ -∞ ∞ ] ]

--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 [ [ -∞ ∞ ] ]

--consensus / NA

1000G consensus mode
This argument is specifically intended for 1000G consensus analysis mode. Setting this flag will inject all provided alleles to the assembly graph but will not forcibly genotype all of them.

boolean false

--contamination-fraction-per-sample-file / -contamination-file

Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be "" (Contamination is double) per line; No header.
This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples. Samples that do not appear in this file will be processed with CONTAMINATION_FRACTION.

File null

--contamination-fraction-to-filter / -contamination

Fraction of contamination in sequencing data (for all samples) to aggressively remove
If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads. Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we will try to remove (N * contamination fraction) bases for each alternate allele.

double 0.0 [ [ -∞ ∞ ] ]

--contamination-table / NA

Table containing contamination information.

File null

--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

--debug / -debug

Print out very verbose debug information about each triggering active region

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 [ [ -∞ ∞ ] ]

--do-not-run-physical-phasing / NA

Disable physical phasing
As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.

boolean false

--dont-increase-kmer-sizes-for-cycles / NA

Disable iterating over kmer sizes when graph cycles are detected
When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are resolved. Disabling this behavior may cause the program to give up on assembling the ActiveRegion.

boolean false

--dont-trim-active-regions / NA

If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping

boolean false

--dont-use-soft-clipped-bases / NA

Do not analyze soft clipped bases in the reads

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] []

--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 [ [ -∞ ∞ ] ]

--genotype-filtered-alleles / NA

Whether to genotype all given alleles, even filtered ones, --genotyping_mode is GENOTYPE_GIVEN_ALLELES
When set to true an when in GENOTYPE_GIVEN_ALLELES mode all given alleles, even filtered ones, are genotyped

boolean false

--genotyping-mode / NA

Specifies how to determine the alternate alleles to use for genotyping

The --genotyping-mode argument is an enumerated type (GenotypingOutputMode), which can have one of the following values:

DISCOVERY: The genotyper will choose the most likely alternate allele
GENOTYPE_GIVEN_ALLELES: Only the alleles passed by the user should be considered.

GenotypingOutputMode DISCOVERY

--graph-output / -graph

Write debug assembly graph information to this file
This argument is meant for debugging and is not immediately useful for normal analysis use.

String null

--help / -h

display the help message

boolean false

--heterozygosity / NA

Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries.

Double 0.001 [ [ -∞ ∞ ] ]

--heterozygosity-stdev / NA

Standard deviation of heterozygosity for SNP and indel calling.
The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the *mean* of this distribution; this parameter gives its spread.

double 0.01 [ [ -∞ ∞ ] ]

--indel-heterozygosity / NA

Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
This argument informs the prior probability of having an indel at a site.

double 1.25E-4 [ [ -∞ ∞ ] ]

--input / -I

BAM/SAM/CRAM file containing reads

List[String] []

--input-prior / NA

Input prior for calls
By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model, see e.g. Waterson (1975) or Tajima (1996). This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N There are instances where using this prior might not be desireable, e.g. for population studies where prior might not be appropriate, as for example when the ancestral status of the reference allele is not known. By using this argument, user can manually specify priors to be used for calling as a vector for doubles, with the following restriciotns: a) User must specify 2N values, where N is the number of samples. b) Only diploid calls supported. c) Probability values are specified in double format, in linear space. d) No negative values allowed. e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one. f) If user-defined values add to more than one, an error will be produced. If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g. --input-prior 0.33 --input-prior 0.33 for the single-sample diploid case.

List[Double] []

--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] []

--kmer-size / NA

Kmer size to use in the read threading assembler
Multiple kmer sizes can be specified, using e.g. `--kmer-size 10 --kmer-size 25`.

List[Integer] [10, 25]

--lenient / -LE

Lenient processing of VCF files

boolean false

--log-somatic-prior / NA

Prior probability that a given site has a somatic allele.
Prior log-10 probability that any given site has a somatic allele. Impacts germline probability calculation. The workflow uses this parameter only towards the germline event filter. It does NOT relate to the LOD threshold. For example, -6 translates to one in a million or ~3000 somatic mutations per human genome. Depending on tumor type, mutation rate ranges vary (Lawrence et al. Nature 2013), and so adjust parameter accordingly. For higher expected rate of mutation, adjust number up, e.g. -5. For lower expected rate of mutation, adjust number down, e.g. -7.

double -6.0 [ [ -∞ ∞ ] ]

--max-alt-allele-count / NA

filter variants with too many alt alleles

int 1 [ [ -∞ ∞ ] ]

--max-alternate-alleles / NA

Maximum number of alternate alleles to genotype
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter. See also {@link #MAX_GENOTYPE_COUNT}.

int 6 [ [ -∞ ∞ ] ]

--max-contamination-probability / NA

Filter variants with posterior probability to be due to contamination greater than this.

double 0.1 [ [ -∞ ∞ ] ]

--max-events-in-region / NA

Variants coming from an assembly region with more than this many events are filtered

int 2 [ [ -∞ ∞ ] ]

--max-genotype-count / NA

Maximum number of genotypes to consider at any site
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used. The possible genotypes are simply different ways of partitioning alleles given a specific ploidy asumption. Therefore, we remove genotypes from consideration by removing alternate alleles that are the least well supported. The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step. Note that the reference allele is always kept. Note that genotyping sites with large genotype counts is both CPU and memory intensive. Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter. The maximum number of alternative alleles used in the genotyping step will be the lesser of the two: 1. the largest number of alt alleles, given ploidy, that yields a genotype count no higher than {@link #MAX_GENOTYPE_COUNT} 2. the value of {@link #MAX_ALTERNATE_ALLELES} See also {@link #MAX_ALTERNATE_ALLELES}.

int 1024 [ [ -∞ ∞ ] ]

--max-germline-posterior / NA

Maximum posterior probability that an allele is a germline variant

double 0.1 [ [ -∞ ∞ ] ]

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

filter variants for which alt reads' median fragment length is very different from the median for ref reads.

int 10000 [ [ -∞ ∞ ] ]

--max-num-haplotypes-in-population / NA

Maximum number of haplotypes to consider for your population
The assembly graph can be quite complex, and could imply a very large number of possible haplotypes. Each haplotype considered requires N PairHMM evaluations if there are N reads across all samples. In order to control the run of the haplotype caller we only take maxNumHaplotypesInPopulation paths from the graph, in order of their weights, no matter how many paths are possible to generate from the graph. Putting this number too low will result in dropping true variation because paths that include the real variant are not even considered. You can consider increasing this number when calling organisms with high heterozygosity.

int 128 [ [ -∞ ∞ ] ]

--max-strand-artifact-probability / -strand-prob

Filter a variant if the probability of strand artifact exceeds this number

double 0.99 [ [ -∞ ∞ ] ]

--min-base-quality-score / -mbq

Minimum base quality required to consider a base for calling
Bases with a quality below this threshold will not be used for calling.

byte 10 [ [ -∞ ∞ ] ]

--min-dangling-branch-length / NA

Minimum length of a dangling branch to attempt recovery
When constructing the assembly graph we are often left with "dangling" branches. The assembly engine attempts to rescue these branches by merging them back into the main graph. This argument describes the minimum length of a dangling branch needed for the engine to try to rescue it. A smaller number here will lead to higher sensitivity to real variation but also to a higher number of false positives.

int 4 [ [ -∞ ∞ ] ]

--min-median-base-quality / NA

filter variants for which alt reads' median base quality is too low.

int 20 [ [ -∞ ∞ ] ]

--min-median-mapping-quality / NA

filter variants for which alt reads' median mapping quality is too low.

int 30 [ [ -∞ ∞ ] ]

--min-median-read-position / NA

filter variants for which the median position of alt alleles within reads is too near the end of reads.

int 5 [ [ -∞ ∞ ] ]

--min-pcr-slippage-size / NA

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

int 8 [ [ -∞ ∞ ] ]

--min-pruning / NA

Minimum support to not prune paths in the graph
Paths with fewer supporting kmers than the specified threshold will be pruned from the graph. Be aware that this argument can dramatically affect the results of variant calling and should only be used with great caution. Using a prune factor of 1 (or below) will prevent any pruning from the graph, which is generally not ideal; it can make the calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph). Higher values tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher depth to produce calls).

int 2 [ [ -∞ ∞ ] ]

--min-strand-artifact-allele-fraction / -strand-af

Only filter a variant if the MAP estimate of allele fraction given artifact is below this number

double 0.01 [ [ -∞ ∞ ] ]

--native-pair-hmm-threads / NA

How many threads should a native pairHMM implementation use

int 4 [ [ -∞ ∞ ] ]

--native-pair-hmm-use-double-precision / NA

use double precision in the native pairHmm. This is slower but matches the java implementation better

boolean false

--normal-artifact-lod / NA

LOD threshold for calling normal artifacts
This is a measure of the minimum evidence to support that a variant observed in the tumor is not also present in the normal as an artifact i.e. not as a germline event.

double 0.0 [ [ -∞ ∞ ] ]

--normal-p-value-threshold / NA

P value threshold for normal artifact filter

double 0.001 [ [ -∞ ∞ ] ]

--num-pruning-samples / NA

Number of samples that must pass the minPruning threshold
If fewer samples than the specified number pass the minPruning threshold for a given path, that path will be eliminated from the graph.

int 1 [ [ -∞ ∞ ] ]

--num-reference-samples-if-no-call / NA

Number of hom-ref genotypes to infer at sites not present in a panel
When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength) that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0, AN=2000".

int 0 [ [ -∞ ∞ ] ]

--orientation-bias-fdr / NA

Mutect will calculate the threshold for the read orientation filter such that the FDR doesn't exceed this value
We set the filtering threshold for the read orientation filter such that the false discovery rate (FDR), which equals the ratio of expected number of false positives due to read orientation artifact to the total number of variants does not exceed this value.

double 0.05 [ [ -∞ ∞ ] ]

--output / -O

The output filtered VCF file

R String null

--output-mode / NA

Specifies which type of calls we should output

The --output-mode argument is an enumerated type (OutputMode), which can have one of the following values:

EMIT_VARIANTS_ONLY: produces calls only at variant sites
EMIT_ALL_CONFIDENT_SITES: produces calls at variant sites and confident reference sites
EMIT_ALL_SITES: produces calls at any callable site regardless of confidence; this argument is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode

OutputMode EMIT_VARIANTS_ONLY

--pair-hmm-gap-continuation-penalty / NA

Flat gap continuation penalty for use in the Pair HMM

int 10 [ [ -∞ ∞ ] ]

--pair-hmm-implementation / -pairHMM

The PairHMM implementation to use for genotype likelihood calculations
The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.

The --pair-hmm-implementation argument is an enumerated type (Implementation), which can have one of the following values:

EXACT
ORIGINAL
LOGLESS_CACHING
AVX_LOGLESS_CACHING
AVX_LOGLESS_CACHING_OMP
EXPERIMENTAL_FPGA_LOGLESS_CACHING
FASTEST_AVAILABLE

Implementation FASTEST_AVAILABLE

--pcr-indel-model / NA

The PCR indel model to use
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts. The correction is based on the reference context, and acts specifically around repetitive sequences that tend to cause PCR errors). The variant likelihoods are penalized in increasing scale as the context around a putative indel is more repetitive (e.g. long homopolymer). The correction can be disabling by specifying '-pcrModel NONE'; in that case the default base insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator). VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE.

The --pcr-indel-model argument is an enumerated type (PCRErrorModel), which can have one of the following values:

NONE: no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used
HOSTILE: a most aggressive model will be applied that sacrifices true positives in order to remove more false positives
AGGRESSIVE: a more aggressive model will be applied that sacrifices true positives in order to remove more false positives
CONSERVATIVE: a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives

PCRErrorModel CONSERVATIVE

--pcr-slippage-p-value / NA

P-value threshold for PCR slippage

double 0.001 [ [ -∞ ∞ ] ]

--pcr-slippage-rate / NA

In contexts where PCR slippage is suspected, the rough fraction of reads in which slippage occurs

double 0.1 [ [ -∞ ∞ ] ]

--phred-scaled-global-read-mismapping-rate / NA

The global assumed mismapping rate for reads
The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their mapping quality. This term effects the probability that a read originated from the reference haplotype, regardless of its edit distance from the reference, in that the read could have originated from the reference haplotype but from another location in the genome. Suppose a read has many mismatches from the reference, say like 5, but has a very high mapping quality of 60. Without this parameter, the read would contribute 5 * Q30 evidence in favor of its 5 mismatch haplotype compared to reference, potentially enough to make a call off that single read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype that this (and any) read could contribute is Q30. Set this term to any negative number to turn off the global mapping rate.

int 45 [ [ -∞ ∞ ] ]

--population-callset / -population

Callset to use in calculating genotype priors
Supporting external panel. Allele counts from this panel (taken from AC,AN or MLEAC,AN or raw genotypes) will be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later. Note that unlike CalculateGenotypePosteriors, HaplotypeCaller only allows one supporting callset.

FeatureInput[VariantContext] null

--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

--recover-dangling-heads / NA

This argument is deprecated since version 3.3
As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details.

boolean false

--reference / -R

Reference sequence

String null

--sample-ploidy / -ploidy

Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy

int 2 [ [ -∞ ∞ ] ]

--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

--smith-waterman / NA

Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice

The --smith-waterman argument is an enumerated type (Implementation), which can have one of the following values:

FASTEST_AVAILABLE: use the fastest available Smith-Waterman aligner that runs on your hardware
AVX_ENABLED: use the AVX enabled Smith-Waterman aligner
JAVA: use the pure java implementation of Smith-Waterman, works on all hardware

Implementation JAVA

--standard-min-confidence-threshold-for-calling / -stand-call-conf

The minimum phred-scaled confidence threshold at which variants should be called
The minimum phred-scaled confidence threshold at which variants should be called. Only variant sites with QUAL equal or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode (using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding will then be performed in the subsequent GenotypeGVCFs command.

double 10.0 [ [ -∞ ∞ ] ]

--stats / NA

Write the filtering statistics to this file

File Mutect2FilteringStats.tsv

--TMP_DIR / NA

Undocumented option

List[File] []

--tumor-lod / NA

LOD threshold for calling tumor variant
Only variants with tumor LODs exceeding this threshold can pass filtering.

double 5.3 [ [ -∞ ∞ ] ]

--tumor-segmentation / NA

Pileup summaries for the tumor sample as output by CalculateContamination
A table containing tumor segments and the minor allele fraction of germline hets within each segment. This allows us to refine the germline event filter by, for example, not filtering an allele with an allele fraction significantly different from 0.5 in a segment where the minor allele fraction is 0.5.

File null

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

Filter a variant if a site contains fewer than this many unique (i.e. deduplicated) reads supporting the alternate allele

int 0 [ [ -∞ ∞ ] ]

--use-filtered-reads-for-annotations / NA

Use the contamination-filtered read maps for the purposes of annotating variants

boolean false

--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

--use-new-qual-calculator / -new-qual

If provided, we will use the new AF model instead of the so-called exact model
Use the new allele frequency / QUAL score model

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 4.0.8.0 built at 25-51-2019 10:51:39.

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Category Variant Filtering

Overview

Usage example

FilterMutectCalls specific arguments

Argument details

--add-output-sam-program-record / -add-output-sam-program-record

--add-output-vcf-command-line / -add-output-vcf-command-line

--all-site-pls / NA

--alleles / NA

--allow-non-unique-kmers-in-ref / NA

--annotate-with-num-discovered-alleles / NA

--arguments_file / NA

--bam-output / -bamout

--bam-writer-type / NA

--base-quality-score-threshold / NA

--cloud-index-prefetch-buffer / -CIPB

--cloud-prefetch-buffer / -CPB

--consensus / NA

--contamination-fraction-per-sample-file / -contamination-file

--contamination-fraction-to-filter / -contamination

--contamination-table / NA

--create-output-bam-index / -OBI

--create-output-bam-md5 / -OBM

--create-output-variant-index / -OVI

--create-output-variant-md5 / -OVM

--debug / -debug

--disable-bam-index-caching / -DBIC

--disable-read-filter / -DF

--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation

--disable-tool-default-read-filters / -disable-tool-default-read-filters

--distance-on-haplotype / NA

--do-not-run-physical-phasing / NA

--dont-increase-kmer-sizes-for-cycles / NA

--dont-trim-active-regions / NA

--dont-use-soft-clipped-bases / NA

--exclude-intervals / -XL

--gatk-config-file / NA

--gcs-max-retries / -gcs-retries

--genotype-filtered-alleles / NA

--genotyping-mode / NA

--graph-output / -graph

--help / -h

--heterozygosity / NA

--heterozygosity-stdev / NA

--indel-heterozygosity / NA

--input / -I

--input-prior / NA

--interval-exclusion-padding / -ixp

--interval-merging-rule / -imr

--interval-padding / -ip

--interval-set-rule / -isr

--intervals / -L

--kmer-size / NA

--lenient / -LE

--log-somatic-prior / NA

--max-alt-allele-count / NA

--max-alternate-alleles / NA

--max-contamination-probability / NA

--max-events-in-region / NA

--max-genotype-count / NA

--max-germline-posterior / NA

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

--max-num-haplotypes-in-population / NA

--max-strand-artifact-probability / -strand-prob

--min-base-quality-score / -mbq

--min-dangling-branch-length / NA

--min-median-base-quality / NA

--min-median-mapping-quality / NA

--min-median-read-position / NA

--min-pcr-slippage-size / NA

--min-pruning / NA

--min-strand-artifact-allele-fraction / -strand-af

--native-pair-hmm-threads / NA

--native-pair-hmm-use-double-precision / NA

--normal-artifact-lod / NA

--normal-p-value-threshold / NA