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
GATK version 4.1.0.0 built at Sat, 23 Nov 2019 17:12:18 -0500.
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