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ExtendedFuncotator

Functional Annotator

Category Public/Stable Tools

Overview

This is an extension of the GATK Funcotator tool. The primary purpose of this tool is to produce a VCF output where specific fields from Funcotator are output as discrete INFO field annotations, rather than Funcotator's default, which involves a single INFO field where the annotations are concatenated together.

Usage example:

  java -jar DISCVRseq.jar ExtendedFuncotator \
     -V input.vcf.gz \
     -R myFasta.fasta \
     --ref-version hg19 \
     --data-sources-path ./path/to/dataSource \
     -cf configFile.txt \
     -O output.annotated.vcf.gz

The config file must specify the list of Funcotator fields to include, and the VCF info attributes for each. The fields ID, Number, Type, and Description must match valid VCF header values.

    DataSource	SourceField	ID	Number	Type	Description
    testSource	OtherField	f1	UNBOUNDED	String	This is field1
    testSource	ExpectedResult	f2	UNBOUNDED	String	This is field2
    vcfTestSource	AA	f3	A	Float	This is field3
    vcfTestSource	BB	f4	UNBOUNDED	String	This is field4

Additional Information

Genome/Reference Files

Please note that if this tools uses a reference genome, that FASTA must be indexed with samtools and to have a sequence dictionary created with Picard. See here for more information

Read filters

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

WellformedReadFilter

ExtendedFuncotator 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
--config-file -cf	null	A TSV file specifying the Funcotator fields to extract, and their VCF INFO field annotation information.
--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	null	Output file to which annotated variants should be written.
--output-file-format	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.
--ref-version	null	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	null	Reference sequence file
--variant -V	null	A VCF file containing variants
Optional Tool Arguments
--annotation-default	[]	Annotations to include in all annotated variants if the annotation is not specified in the data sources (in the format :). This will add the specified annotation to every annotated variant if it is not already present.
--annotation-override	[]	Override values for annotations (in the format :). Replaces existing annotations of the given name with given values.
--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	null	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.
--five-prime-flank-size	5000	Variants within this many bases of the 5' end of a transcript (and not overlapping any part of the transcript itself) will be annotated as being in the 5' flanking region of that transcript
--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.
--print-missing-fields -pmf	false	If specified, a list of all fields present in the data sources but not included in the output will be printed, and the tool will immediately exit.
--reannotate-vcf	false	When input VCF has already been annotated, still annotate again.
--remove-filtered-variants	false	Ignore/drop variants that have been filtered in the input. These variants will not appear in the output file.
--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).
--three-prime-flank-size	0	Variants within this many bases of the 3' end of a transcript (and not overlapping any part of the transcript itself) will be annotated as being in the 3' flanking region of that transcript
--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	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
--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	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
--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
--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

--annotation-default / NA

Annotations to include in all annotated variants if the annotation is not specified in the data sources (in the format :). This will add the specified annotation to every annotated variant if it is not already present.

List[String] []

--annotation-override / NA

Override values for annotations (in the format :). Replaces existing annotations of the given name with given values.

List[String] []

--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 [ [ -∞ ∞ ] ]

--config-file / -cf

A TSV file specifying the Funcotator fields to extract, and their VCF INFO field annotation information.

R GATKPath 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

--custom-variant-classification-order / NA

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

--data-sources-path / NA

The path to a data source folder for Funcotator. May be specified more than once to handle multiple data source folders.

R List[String] []

--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

--exclude-field / NA

Fields that should not be rendered in the final output. Only exact name matches will be excluded.

Set[String] []

--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). strings gathered from the command line -XL argument to be parsed into intervals to exclude

List[String] []

--five-prime-flank-size / NA

Variants within this many bases of the 5' end of a transcript (and not overlapping any part of the transcript itself) will be annotated as being in the 5' flanking region of that transcript

int 5000 [ [ -∞ ∞ ] ]

--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. User must have storage.buckets.get permission on the bucket being accessed.

String ""

--help / -h

display the help message

boolean false

--input / -I

BAM/SAM/CRAM file containing reads

List[GATKPath] []

--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
INTERSECTION

IntervalSetRule UNION

--intervals / -L

One or more genomic intervals over which to operate

List[String] []

--lenient / -LE

Lenient processing of VCF files

boolean false

--lookahead-cache-bp / NA

Number of base-pairs to cache when querying variants. Can be overridden in individual data source configuration files.

int 100000 [ [ 0 ∞ ] ]

--max-variants-per-shard / NA

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int 0 [ [ 0 ∞ ] ]

--min-num-bases-for-segment-funcotation / NA

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 / -O

Output file to which annotated variants should be written.

R File null

--output-file-format / NA

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:

VCF
MAF
SEG

R OutputFormatType null

--print-missing-fields / -pmf

If specified, a list of all fields present in the data sources but not included in the output will be printed, and the tool will immediately exit.

boolean false

--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[GATKPath] []

--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

--reannotate-vcf / NA

When input VCF has already been annotated, still annotate again.

boolean false

--ref-version / NA

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 / -R

Reference sequence file

R GATKPath null

--remove-filtered-variants / NA

Ignore/drop variants that have been filtered in the input. These variants will not appear in the output file.

boolean false

--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.

GATKPath 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

--splice-site-window-size / NA

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 ∞ ] ]

--three-prime-flank-size / NA

Variants within this many bases of the 3' end of a transcript (and not overlapping any part of the transcript itself) will be annotated as being in the 3' flanking region of that transcript

int 0 [ [ -∞ ∞ ] ]

--tmp-dir / NA

Temp directory to use.

GATKPath null

--transcript-list / NA

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] []