Make a panel of normals for use with Mutect2
The tool takes multiple normal sample callsets produced by {@link Mutect2}'s tumor-only mode and collates sites present in multiple samples (two by default, set by the --min-sample-count argument) into a sites-only VCF. The PoN captures common artifacts. Mutect2 then uses the PoN to filter variants at the site-level. The --max-germline-probability argument sets the threshold for possible germline variants to be included in the PoN. By default this is set to 0.5, so that likely germline events are excluded. This is usually the correct behavior as germline variants are best handled by probabilistic modeling via Mutect2's --germline-resource argument. A germline resource, such as gnomAD in the case of humans, is a much more refined tool for germline filtering than any PoN could be.
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.
Note that as of May, 2019 -max-mnp-distance must be set to zero to avoid a bug in GenomicsDBImport.
gatk Mutect2 -R reference.fasta -I normal1.bam -max-mnp-distance 0 -O normal1.vcf.gz
gatk GenomicsDBImport -R reference.fasta -L intervals.interval_list \
--genomicsdb-workspace-path pon_db \
-V normal1.vcf.gz \
-V normal2.vcf.gz \
-V normal3.vcf.gz
gatk CreateSomaticPanelOfNormals -R reference.fasta -V gendb://pon_db -O pon.vcf.gz
This Read Filter is automatically applied to the data by the Engine before processing by CreateSomaticPanelOfNormals.
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 |
Output vcf | ||
| --variant -V |
A VCF file containing variants | ||
| Optional Tool Arguments | |||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --call-genotypes |
false | Output called genotypes in final VCF (otherwise no-call) | |
| --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). | |
| --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! | |
| --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. User must have storage.buckets.get permission on the bucket being accessed. | ||
| --genomicsdb-max-alternate-alleles |
50 | Maximum number of alternate alleles that will be combined on reading from GenomicsDB | |
| --genomicsdb-shared-posixfs-optimizations |
false | Allow for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre). If set, file level locking is disabled and file system writes are minimized. | |
| --genomicsdb-use-gcs-hdfs-connector |
false | Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs. | |
| --germline-resource |
Population vcf of germline sequencing containing allele fractions. | ||
| --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 | ||
| --max-germline-probability |
0.5 | Skip genotypes with germline probability greater than this value | |
| --min-sample-count |
2 | Number of samples containing a variant site required to include it in the panel of normals. | |
| --reference -R |
Reference sequence | ||
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --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 |
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 | |
| --inverted-read-filter -XRF |
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters). | ||
| --lenient -LE |
false | Lenient processing of VCF files | |
| --max-variants-per-shard |
0 | If non-zero, partitions VCF output into shards, each containing up to the given number of records. | |
| --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 |
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | ||
| --tmp-dir |
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 | |||
| --genomicsdb-use-bcf-codec |
false | Use BCF Codec Streaming for data from GenomicsDB instead of the default VCFCodec. BCFCodec performs slightly better but currently does not support 64-bit width positions and INFO fields and for computed annotation sizes to exceed 32-bit integer space. | |
| --showHidden |
false | display hidden arguments | |
| --variant-output-filtering |
Restrict the output variants to ones that match the specified intervals according to the specified matching mode. | ||
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
read one or more arguments files and add them to the command line
List[File] []
Output called genotypes in final VCF (otherwise no-call)
Output called genotypes in the final VCF (otherwise no-call)
boolean false
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean 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.
boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
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). strings gathered from the command line -XL argument to be parsed into intervals to exclude
List[String] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
String ""
Maximum number of alternate alleles that will be combined on reading from GenomicsDB
Maximum number of alternate alleles that will report likelihoods after being combined on reading from GenomicsDB (including )
Must be at least one greater than the maximum number of alternate alleles for genotyping. A typical value is 3 more than the --max-alternate-alleles value that's used by GenotypeGVCFs and larger differences
result in more robustness to PCR-related indel errors.
NOTE: GenotypeGVCFs will drop multi-allelic sites with more than this many alternate alleles since they are missing likelihoods.
See also
int 50 [ [ -∞ ∞ ] ]
Allow for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre). If set, file level locking is disabled and file system writes are minimized.
boolean false
Use BCF Codec Streaming for data from GenomicsDB instead of the default VCFCodec. BCFCodec performs slightly better but currently does not support 64-bit width positions and INFO fields and for computed annotation sizes to exceed 32-bit integer space.
Currently there is no support for 64-bit fields in BCF2Codec. The VCFCodec allows for 64-bit
width positions and INFO fields and for computed annotation sizes to exceed the 32-bit
integer space while encoding/decoding with GenomicsDB. Use the BCF2Codec option if and
only if performance is an issue.
boolean false
Use the GCS HDFS Connector instead of the native GCS SDK client with gs:// URLs.
boolean false
Population vcf of germline sequencing containing allele fractions.
A resource, such as gnomAD, containing population allele frequencies of common and rare variants. We use this to remove germline variants from the panel
of normals, keeping only technical artifacts
FeatureInput[VariantContext] null
display the help message
boolean false
BAM/SAM/CRAM file containing reads
List[GATKPath] []
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 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:
IntervalMergingRule ALL
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 [ [ -∞ ∞ ] ]
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:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
Lenient processing of VCF files
boolean false
Skip genotypes with germline probability greater than this value
double 0.5 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
Number of samples containing a variant site required to include it in the panel of normals.
int 2 [ [ -∞ ∞ ] ]
Output vcf
R String null
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
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:
ValidationStringency SILENT
Reference sequence
GATKPath null
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
A VCF file containing variants
R GATKPath null
Restrict the output variants to ones that match the specified intervals according to the specified matching mode.
The --variant-output-filtering argument is an enumerated type (Mode), which can have one of the following values:
Mode null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.