Functional annotation for segment files. The output formats are not well-defined and subject to change.
Perform functional annotation on a segment file (tsv). Outputs two files. The first is a tsv where each row is a segment and the annotations are the covered genes and which genes+exon is overlapped by the segment breakpoints. The second file has a gene for each row. The rest of the information is the segment on which it is covered. The first file will have the name as specified by the output parameter. The second will have '.gene_list.txt' appended. The functionality here is the same as seen in Oncotator with a SEG file as input, but with both SIMPLE_TSV and GENE_LIST as outputs.
Note that FuncotateSegments will support seg files from the GATK, whereas Oncotator will not.
FuncotateSegments can support hg38 seg files from the GATK.
FuncotateSegments does not support direct reading of cloud-based datasources.
For more information about Oncotator, on small variants, see Ramos AH, Lichtenstein L, et al. Oncotator: Cancer Variant Annotation Tool. Human Mutation (2015). http://dx.doi.org/10.1002/humu.22771
./gatk FuncotateSegments \
--data-sources-path dataSourcesFolder/ \
--ref-version hg19 \
--output-file-format SEG \
-R reference.fasta \
--segments input.seg \
-O input.seg.funcotated.tsv \
--transcript-list tx_list.txt
This Read Filter is automatically applied to the data by the Engine before processing by FuncotateSegments.
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 | |||
| --data-sources-path |
The path to a data source folder for Funcotator. May be specified more than once to handle multiple data source folders. | ||
| --output -O |
Output file to which annotated variants should be written. | ||
| --output-file-format |
The output file format. Either VCF, MAF, or SEG. Please note that MAF output for germline use case VCFs is unsupported. SEG will generate two output files: a simple tsv and a gene list. | ||
| --ref-version |
The version of the Human Genome reference to use (e.g. hg19, hg38, etc.). This will correspond to a sub-folder of each data source corresponding to that data source for the given reference. | ||
| --reference -R |
Reference sequence file | ||
| --segments |
Input segment file (tab-separated values). Must have a call column. | ||
| Optional Tool Arguments | |||
| --alias-to-key-mapping |
[MEAN_LOG2_COPY_RATIO:Segment_Mean, CALL:Segment_Call, sample:Sample, sample_id:Sample, NUM_POINTS_COPY_RATIO:Num_Probes] | (Advanced) Mapping between an alias and key values that are recognized by the backend. Users should not typically have to specify this. | |
| --annotation-default |
Annotations to include in all annotated variants if the annotation is not specified in the data sources (in the format |
||
| --annotation-override |
Override values for annotations (in the format |
||
| --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). | |
| --custom-variant-classification-order |
TSV File containing custom Variant Classification severity map of the form: VARIANT_CLASSIFICATION SEV. VARIANT_CLASSIFICATION must match one of the VariantClassification names (COULD_NOT_DETERMINE, INTRON, FIVE_PRIME_UTR, THREE_PRIME_UTR, IGR, FIVE_PRIME_FLANK, THREE_PRIME_FLANK, MISSENSE, NONSENSE, NONSTOP, SILENT, SPLICE_SITE, IN_FRAME_DEL, IN_FRAME_INS, FRAME_SHIFT_INS, FRAME_SHIFT_DEL, START_CODON_SNP, START_CODON_INS, START_CODON_DEL, DE_NOVO_START_IN_FRAME, DE_NOVO_START_OUT_FRAME, RNA, LINCRNA). SEV is an unsigned integer, where lower is sorted first. When using this option it is HIGHLY recommended you also use the `BEST_EFFECT` transcript selection mode. | ||
| --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! | |
| --exclude-field |
Fields that should not be rendered in the final output. Only exact name matches will be excluded. | ||
| --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. | ||
| --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 | ||
| --lookahead-cache-bp |
100000 | Number of base-pairs to cache when querying variants. Can be overridden in individual data source configuration files. | |
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --splice-site-window-size |
2 | Number of bases on either side of a splice site for a variant to be classified as a SPLICE_SITE variant (default: 2). | |
| --transcript-list |
File to use as a list of transcripts (one transcript ID per line, version numbers are ignored) OR A set of transcript IDs to use for annotation to override selected transcript. | ||
| --transcript-selection-mode |
CANONICAL | Method of detailed transcript selection. This will select the transcript for detailed annotation (CANONICAL, ALL, or BEST_EFFECT). | |
| --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 | |||
| --min-num-bases-for-segment-funcotation |
150 | The minimum number of bases for a variant to be annotated as a segment. Recommended to be changed only for use with FuncotateSegments. Defaults to 150 | |
| --prefer-mane-transcripts |
false | If this flag is set, Funcotator will prefer 'MANE_Plus_Clinical' followed by 'MANE_select' transcripts (including those not tagged 'basic') if one is present for a given variant. If neither tag is present it use the default behavior (only base transcripts). | |
| --showHidden |
false | display hidden arguments | |
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
(Advanced) Mapping between an alias and key values that are recognized by the backend. Users should not typically have to specify this.
Mapping goes from old name to new name. Note that this is not necessarily what is output, since the output
renderer might further transform the name.
List[String] [MEAN_LOG2_COPY_RATIO:Segment_Mean, CALL:Segment_Call, sample:Sample, sample_id:Sample, NUM_POINTS_COPY_RATIO:Num_Probes]
Annotations to include in all annotated variants if the annotation is not specified in the data sources (in the format
List[String] []
Override values for annotations (in the format
List[String] []
read one or more arguments files and add them to the command line
List[File] []
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
TSV File containing custom Variant Classification severity map of the form: VARIANT_CLASSIFICATION SEV. VARIANT_CLASSIFICATION must match one of the VariantClassification names (COULD_NOT_DETERMINE, INTRON, FIVE_PRIME_UTR, THREE_PRIME_UTR, IGR, FIVE_PRIME_FLANK, THREE_PRIME_FLANK, MISSENSE, NONSENSE, NONSTOP, SILENT, SPLICE_SITE, IN_FRAME_DEL, IN_FRAME_INS, FRAME_SHIFT_INS, FRAME_SHIFT_DEL, START_CODON_SNP, START_CODON_INS, START_CODON_DEL, DE_NOVO_START_IN_FRAME, DE_NOVO_START_OUT_FRAME, RNA, LINCRNA). SEV is an unsigned integer, where lower is sorted first. When using this option it is HIGHLY recommended you also use the `BEST_EFFECT` transcript selection mode.
GATKPath null
The path to a data source folder for Funcotator. May be specified more than once to handle multiple data source folders.
R List[String] []
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
Fields that should not be rendered in the final output. Only exact name matches will be excluded.
Set[String] []
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 ""
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
Number of base-pairs to cache when querying variants. Can be overridden in individual data source configuration files.
int 100000 [ [ 0 ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
The minimum number of bases for a variant to be annotated as a segment. Recommended to be changed only for use with FuncotateSegments. Defaults to 150
int 150 [ [ -∞ ∞ ] ]
Output file to which annotated variants should be written.
R File null
The output file format. Either VCF, MAF, or SEG. Please note that MAF output for germline use case VCFs is unsupported. SEG will generate two output files: a simple tsv and a gene list.
The --output-file-format argument is an enumerated type (OutputFormatType), which can have one of the following values:
R OutputFormatType null
If this flag is set, Funcotator will prefer 'MANE_Plus_Clinical' followed by 'MANE_select' transcripts (including those not tagged 'basic') if one is present for a given variant. If neither tag is present it use the default behavior (only base transcripts).
boolean false
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
The version of the Human Genome reference to use (e.g. hg19, hg38, etc.). This will correspond to a sub-folder of each data source corresponding to that data source for the given reference.
R String null
Reference sequence file
R GATKPath null
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Input segment file (tab-separated values). Must have a call column.
R GATKPath null
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
Number of bases on either side of a splice site for a variant to be classified as a SPLICE_SITE variant (default: 2).
int 2 [ [ 0 ∞ ] ]
Temp directory to use.
GATKPath null
File to use as a list of transcripts (one transcript ID per line, version numbers are ignored) OR A set of transcript IDs to use for annotation to override selected transcript.
Set[String] []
Method of detailed transcript selection. This will select the transcript for detailed annotation (CANONICAL, ALL, or BEST_EFFECT).
The --transcript-selection-mode argument is an enumerated type (TranscriptSelectionMode), which can have one of the following values:
TranscriptSelectionMode CANONICAL
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
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.