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DiscvrVariantAnnotator

Tool for adding annotations to VCF files

Category Variant Manipulation

Overview

Annotate variant calls with context information. This is an extension of GATK's VariantAnnotator, and adds a number of custom optional annotations. Usage is essentially identical as GATK's tool.

Input

A variant set to annotate and optionally one or more BAM files.

Output

An annotated VCF.

Usage examples

Annotate a VCF with dbSNP IDs and depth of coverage for each sample

   DiscvrVariantAnnotator \
   -R reference.fasta \
   -I input.bam \
   -V input.vcf \
   -o output.vcf \
   -A Coverage \
   --dbsnp dbsnp.vcf

Annotate a VCF with allele frequency by an external resource. Annotation will only occur if there is allele concordance between the resource and the input VCF

   DiscvrVariantAnnotator \
   -R reference.fasta \
   -I input.bam \
   -V input.vcf \
   -o output.vcf \
   -L anotherInput.vcf \
   --resource foo:resource.vcf \
   -E foo.AF \
   --resource-allele-concordance

Additional annotations include: - GenotypeConcordance: flag genotypes with discordant values relative to a reference VCF - GenotypeConcordanceBySite: Annotate the number of discordant genotypes per site, relative to a reference VCF - MendelianViolationCount: Uses a more extensive check for MVs than default GATK. This annotates the number of MVs and IDs of samples with MVs for each site. - MendelianViolationCountBySample: This is a genotype-level annotation that flags the number of MVs detected per sample. - RefAlleleFrequency:

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

DiscvrVariantAnnotator 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 file to which variants should be written
--variant -V	null	A VCF file containing variants
Optional Tool Arguments
--af-source-vcf -asv	null	Allele frequency source VCF
--annotation -A	[]	One or more specific annotations to add to variant calls
--annotation-group -G	[]	One or more groups of annotations to apply to variant calls
--annotations-to-exclude -AX	[]	One or more specific annotations to exclude from variant calls
--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).
--dbsnp -D	null	dbSNP file
--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!
--expression -E	[]	One or more specific expressions to apply to variant calls
--flow-order-for-annotations	[]	flow order used for this annotations. [readGroup:]flowOrder
--founder-id	[]	Samples representing the population "founders"
--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
--mendelian-violation-qual-threshold	10.0	Minimum GQ score for each trio member to accept a site as a violation
--min-base-quality-score	10	Minimum base quality required to confidently assign a read to an allele
--pedigree -ped	null	Pedigree file for determining the population "founders"
--pedigreeValidationType -pedValidationType	STRICT	The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT
--reference -R	null	Reference sequence
--reference-genotypes-vcf -rg	null	Reference genotypes VCF
--resource	[]	External resource VCF file
--resource-allele-concordance -rac	false	Check for allele concordances when using an external resource VCF file
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--source-info-field-key	AF	Source INFO field key
--target-info-field-key	null	Target INFO field key
--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.
--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-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
--comparison -comp	[]	Comparison VCF file(s)
--disable-tool-default-annotations	false	Disable all tool default annotations
--enable-all-annotations	false	Use all possible annotations (not for the faint of heart)
--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

--af-source-vcf / -asv

Allele frequency source VCF

FeatureInput[VariantContext] null

--annotation / -A

One or more specific annotations to add to variant calls
Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.

List[String] []

--annotation-group / -G

One or more groups of annotations to apply to variant calls
Which groups of annotations to add to the output variant calls. Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.

List[String] []

--annotations-to-exclude / -AX

One or more specific annotations to exclude from variant calls
Which annotations to exclude from output in the variant calls. Note that this argument has higher priority than the -A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other options.

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 [ [ -∞ ∞ ] ]

--comparison / -comp

Comparison VCF file(s)

List[FeatureInput[VariantContext]] []

--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

--dbsnp / -D

dbSNP file
A dbSNP VCF file.

FeatureInput[VariantContext] null

--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-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-annotations / -disable-tool-default-annotations

Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool

boolean false

--enable-all-annotations / NA

Use all possible annotations (not for the faint of heart)
You can use the -AX argument in combination with this one to exclude specific annotations. Note that some annotations may not be actually applied if they are not applicable to the data provided or if they are unavailable to the tool (e.g. there are several annotations that are currently not hooked up to HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation for individual annotations' requirements).

boolean false

--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] []

--expression / -E

One or more specific expressions to apply to variant calls

Set[String] []

--flow-order-for-annotations / NA

flow order used for this annotations. [readGroup:]flowOrder

List[String] []

--founder-id / -founder-id

Samples representing the population "founders"

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. 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

--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 ∞ ] ]

--mendelian-violation-qual-threshold / NA

Minimum GQ score for each trio member to accept a site as a violation
This argument specifies the genotype quality (GQ) threshold that all members of a trio must have in order for a site to be accepted as a mendelian violation. Note that the `-mv` flag must be set for this argument to have an effect.

double 10.0 [ [ -∞ ∞ ] ]

--min-base-quality-score / NA

Minimum base quality required to confidently assign a read to an allele

byte 10 [ [ -∞ ∞ ] ]

--output / -O

The file to which variants should be written

R File null

--pedigree / -ped

Pedigree file for determining the population "founders"

GATKPath null

--pedigreeValidationType / -pedValidationType

The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT

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

STRICT
SILENT

PedigreeValidationType STRICT

--QUIET / NA

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

Boolean false

--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: