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FilterMutectCalls

Filter somatic SNVs and indels called by Mutect2

Category Variant Filtering


Overview

Filter variants in a Mutect2 VCF callset.

FilterMutectCalls 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
 

Additional Information

Read filters

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

FilterMutectCalls specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Arguments
--output
 -O
null The output filtered VCF file
--variant
 -V
null A VCF file containing variants
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer
 -CIPB
-1 Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloud-prefetch-buffer
 -CPB
40 Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--contamination-estimate
0.0 Estimate of contamination.
--contamination-table
[] 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
--gcs-project-for-requester-pays
"" Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help
 -h
false display the help message
--interval-merging-rule
 -imr
ALL Interval merging rule for abutting intervals
--intervals
 -L
[] One or more genomic intervals over which to operate
--lod-divided-by-depth
0.0035 LOD by depth threshold for filtering variant
--log-somatic-prior
-6.0 Prior probability that a given site has a somatic allele.
--long-indel-length
5 Indels of this length or greater are treated specially by the mapping quality filter.
--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-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
1 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
--mitochondria-mode
false Set filters to mitochondrial defaults
--n-ratio
Infinity Filter a variant if the ratio of Ns to alts in the pileup is greater or equal to this value.
--non-mt-alts-divided-by-alts
0.85 Known NuMT alts by total alts threshold for filtering variant
--normal-artifact-lod
0.0 LOD threshold for calling normal artifacts
--normal-p-value-threshold
0.001 P value threshold for normal artifact filter
--orientation-bias-fdr
0.05 Mutect will calculate the threshold for the read orientation filter such that the FDR doesn't exceed this value
--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
--reference
 -R
null Reference sequence
--sites-only-vcf-output
false If true, don't emit genotype fields when writing vcf file output.
--stats
Mutect2FilteringStats.tsv Write the filtering statistics to this file
--strict-strand-bias
false Always filter if reads are not found in both directions for supporting allele.
--tumor-lod
5.3 LOD threshold for calling variant
--tumor-segmentation
[] 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
--version
false display the version number for this tool
Optional Common Arguments
--add-output-sam-program-record
true If true, adds a PG tag to created SAM/BAM/CRAM files.
--add-output-vcf-command-line
true If true, adds a command line header line to created VCF files.
--create-output-bam-index
 -OBI
true If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5
 -OBM
false If true, create a MD5 digest for any BAM/SAM/CRAM file created
--create-output-variant-index
 -OVI
true If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5
 -OVM
false If true, create a a MD5 digest any VCF file created.
--disable-read-filter
 -DF
[] Read filters to be disabled before analysis
--disable-tool-default-read-filters
false Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
--exclude-intervals
 -XL
[] One or more genomic intervals to exclude from processing
--gatk-config-file
null A configuration file to use with the GATK.
--input
 -I
[] BAM/SAM/CRAM file containing reads
--interval-exclusion-padding
 -ixp
0 Amount of padding (in bp) to add to each interval you are excluding.
--interval-padding
 -ip
0 Amount of padding (in bp) to add to each interval you are including.
--interval-set-rule
 -isr
UNION Set merging approach to use for combining interval inputs
--lenient
 -LE
false Lenient processing of VCF files
--QUIET
false Whether to suppress job-summary info on System.err.
--read-filter
 -RF
[] Read filters to be applied before analysis
--read-index
[] Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
--read-validation-stringency
 -VS
SILENT Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--seconds-between-progress-updates
10.0 Output traversal statistics every time this many seconds elapse
--sequence-dictionary
null Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--tmp-dir
null Temp directory to use.
--use-jdk-deflater
 -jdk-deflater
false Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater
 -jdk-inflater
false Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


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

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true


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

If true, adds a command line header line to created VCF files.

boolean  true


--arguments_file / NA

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

List[File]  []


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

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]


--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]


--contamination-estimate / NA

Estimate of contamination.

double  0.0  [ [ -∞  ∞ ] ]


--contamination-table / NA

Table containing contamination information.

List[File]  []


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

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean  true


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

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false


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

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true


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

If true, create a a MD5 digest any VCF file created.

boolean  false


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

If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.

boolean  false


--disable-read-filter / -DF

Read filters to be disabled before analysis

List[String]  []


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

If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!

boolean  false


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

Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)

boolean  false


--distance-on-haplotype / NA

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

int  100  [ [ -∞  ∞ ] ]


--exclude-intervals / -XL

One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals).

List[String]  []


--gatk-config-file / NA

A configuration file to use with the GATK.

String  null


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

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]


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

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

String  ""


--help / -h

display the help message

boolean  false


--input / -I

BAM/SAM/CRAM file containing reads

List[String]  []


--interval-exclusion-padding / -ixp

Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]


--interval-merging-rule / -imr

Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:

ALL
OVERLAPPING_ONLY

IntervalMergingRule  ALL


--interval-padding / -ip

Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]


--interval-set-rule / -isr

Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:

UNION
Take the union of all intervals
INTERSECTION
Take the intersection of intervals (the subset that overlaps all intervals specified)

IntervalSetRule  UNION


--intervals / -L

One or more genomic intervals over which to operate

List[String]  []


--lenient / -LE

Lenient processing of VCF files

boolean  false


--lod-divided-by-depth / NA

LOD by depth threshold for filtering variant
Only variants with LOD divided by depth exceeding this threshold can pass filtering.

double  0.0035  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--long-indel-length / NA

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

int  5  [ [ -∞  ∞ ] ]


--max-alt-allele-count / NA

filter variants with too many alt alleles

int  1  [ [ -∞  ∞ ] ]


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

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

double  0.99  [ [ -∞  ∞ ] ]


--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  1  [ [ -∞  ∞ ] ]


--min-pcr-slippage-size / NA

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

int  8  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--mitochondria-mode / NA

Set filters to mitochondrial defaults
Mitochondria mode includes "LOD by depth" and "Non MT alt reads by alt reads" filters, which are not included without mitochondria mode. Mitochondria mode only runs the following filters: Insufficient Evidence Filter Duplicated Alt Read Filter Strand Artifact Filter Base Quality Filter Mapping Quality Filter Chimeric Original Alignment Filter LOD by depth Filter Contamination Filter

boolean  false


--n-ratio / NA

Filter a variant if the ratio of Ns to alts in the pileup is greater or equal to this value.

double  Infinity  [ [ -∞  ∞ ] ]


--non-mt-alts-divided-by-alts / NA

Known NuMT alts by total alts threshold for filtering variant
Only variants with alt reads originally aligned outside of the mitochondria (known NuMTs) divided by total alt reads exceeding this threshold can pass filtering.

double  0.85  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--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


--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  [ [ -∞  ∞ ] ]


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--read-filter / -RF

Read filters to be applied before analysis

List[String]  []


--read-index / -read-index

Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.

List[String]  []


--read-validation-stringency / -VS

Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  SILENT


--reference / -R

Reference sequence

String  null


--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]


--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--sites-only-vcf-output / NA

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

boolean  false


--stats / NA

Write the filtering statistics to this file

File  Mutect2FilteringStats.tsv


--strict-strand-bias / NA

Always filter if reads are not found in both directions for supporting allele.

boolean  false


--tmp-dir / NA

Temp directory to use.

String  null


--tumor-lod / NA

LOD threshold for calling variant
Only variants with log odds ratios 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.

List[File]  []


--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-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false


--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false


--variant / -V

A VCF file containing variants

R String  null


--verbosity / -verbosity

Control verbosity of logging.

The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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