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. | |
--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 eterozygosity 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 |
0.025 | 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-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 | |
--output-mode |
EMIT_VARIANTS_ONLY | Specifies which type of calls we should output | |
--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). | |
--standard-min-confidence-threshold-for-calling -stand-call-conf |
10.0 | The minimum phred-scaled confidence threshold at which variants should be called | |
--tumor-lod |
5.3 | LOD threshold for calling tumor variant | |
--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-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
--disable-tool-default-read-filters |
false | Disable all tool default read filters | |
--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 | |
--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 | |
--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
boolean false
--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 [ [ -∞ ∞ ] ]
--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 eterozygosity 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.
-inputPrior 0.33 -inputPrior 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. `-kmerSize 10 -kmerSize 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.
//TODO Note that Mutect2 uses this for the germline annotation while FilterMutectCalls uses this for the contamination filter.
//TODO This duplication is awkward and can probably be addressed by moving some of the germline code into filtering
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
The default value of this argument was chosen to achieve roughly one false positive per covered megabase according
to a back-of-the-envelope calculation assuming the neutral model of allele selection, with parameters estimated from ExAC.
double 0.025 [ [ -∞ ∞ ] ]
--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-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 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--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
--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 [ [ -∞ ∞ ] ]
--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
--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 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--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
GATK version 4.0.2.0 built at 02-13-2019 02:13:49.
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