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**BETA** VariantEval

General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)

Category Variant Evaluation and Refinement


Overview

Given a variant callset, it is common to calculate various quality control metrics. These metrics include the number of raw or filtered SNP counts; ratio of transition mutations to transversions; concordance of a particular sample's calls to a genotyping chip; number of s per sample; etc. Furthermore, it is often useful to stratify these metrics by various criteria like functional class (missense, nonsense, silent), whether the site is CpG site, the amino acid degeneracy of the site, etc. VariantEval facilitates these calculations in two ways: by providing several built-in evaluation and stratification modules, and by providing a framework that permits the easy development of new evaluation and stratification modules.

Input

One or more variant sets to evaluate plus any number of comparison sets.

Output

Evaluation tables detailing the results of the eval modules which were applied. For example:

 output.eval.grp:
 ##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
 CountVariants  CompFeatureInput  CpG      EvalFeatureInput  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate ...
 CountVariants  dbsnp             CpG      eval              none            all      65900028        135770       0         135770        0.00206024  ...
 CountVariants  dbsnp             CpG      eval              none            known    65900028        47068        0         47068         0.00071423  ...
 CountVariants  dbsnp             CpG      eval              none            novel    65900028        88702        0         88702         0.00134601  ...
 CountVariants  dbsnp             all      eval              none            all      65900028        330818       0         330818        0.00502000  ...
 CountVariants  dbsnp             all      eval              none            known    65900028        120685       0         120685        0.00183133  ...
 CountVariants  dbsnp             all      eval              none            novel    65900028        210133       0         210133        0.00318866  ...
 CountVariants  dbsnp             non_CpG  eval              none            all      65900028        195048       0         195048        0.00295976  ...
 CountVariants  dbsnp             non_CpG  eval              none            known    65900028        73617        0         73617         0.00111710  ...
 CountVariants  dbsnp             non_CpG  eval              none            novel    65900028        121431       0         121431        0.00184265  ...
 ...
 

Usage examples

 gatk VariantEval \
   -R reference.fasta \
   -O output.eval.grp \
   --eval set1:set1.vcf \
   --eval set2:set2.vcf \
   [--comp comp.vcf]
 
Count Mendelian violations for each family in a callset with multiple families (and provided pedigree)
 gatk VariantEval \
   -R reference.fasta \
   -O output.MVs.byFamily.table \
   --eval multiFamilyCallset.vcf \
   -no-ev -noST \
   -ST Family \
   -EV MendelianViolationEvaluator
 

Caveat

Some stratifications and evaluators are incompatible with each other due to their respective memory requirements, such as AlleleCount and VariantSummary, or Sample and VariantSummary. If you specify such a combination, the program will output an error message and ask you to disable one of these options. We do not currently provide an exhaustive list of incompatible combinations, so we recommend trying out combinations that you are interested in on a dummy command line, to rapidly ascertain whether it will work or not.

VariantEval 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
--eval
[] Input evaluation file(s)
--output
 -O
null File to which variants should be written
Optional Tool Arguments
--ancestral-alignments
 -aa
null Fasta file with ancestral alleles
--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).
--comp
[] Input comparison file(s)
--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!
--do-not-use-all-standard-modules
 -no-ev
false Do not use the standard modules by default (instead, only those that are specified with the -EV option)
--do-not-use-all-standard-stratifications
 -no-st
false Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
--eval-module
 -EV
[] One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)
--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.
--gold-standard
 -gold
null Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison
--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
--keep-ac0
false If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes
--known-cnvs
null File containing tribble-readable features describing a known list of copy number variants
--KNOWN_NAMES
 -known-name
[] Name of feature bindings containing variant sites that should be treated as known when splitting eval features into known and novel subsets
--list
 -ls
false List the available eval modules and exit
--mendelian-violation-qual-threshold
 -mvq
50.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.
--merge-evals
false If provided, all -eval tracks will be merged into a single eval track
--min-phase-quality
 -mpq
10.0 Minimum phasing quality
--pedigree
 -ped
null Pedigree file for determining the population "founders"
--reference
 -R
null Reference sequence
--require-strict-allele-match
 -strict
false If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping
--sample
 -sn
[] Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
--sample-ploidy
 -ploidy
2 Per-sample ploidy (number of chromosomes per sample)
--SELECT_EXPS
 -select
[] One or more stratifications to use when evaluating the data
--SELECT_NAMES
 -select-name
[] Names to use for the list of stratifications (must be a 1-to-1 mapping)
--sites-only-vcf-output
false If true, don't emit genotype fields when writing vcf file output.
--strat-intervals
null File containing tribble-readable features for the IntervalStratificiation
--stratification-module
 -ST
[] One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
--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
--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
--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


--ancestral-alignments / -aa

Fasta file with ancestral alleles

File  null


--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  [ [ -∞  ∞ ] ]


--comp / -comp

Input comparison file(s)
The variant file(s) to compare against.

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


--do-not-use-all-standard-modules / -no-ev

Do not use the standard modules by default (instead, only those that are specified with the -EV option)

Boolean  false


--do-not-use-all-standard-stratifications / -no-st

Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)

Boolean  false


--eval / -eval

Input evaluation file(s)
The variant file(s) to evaluate.

R List[FeatureInput[VariantContext]]  []


--eval-module / -EV

One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noEV is specified)
See the -list argument to view available modules.

List[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).

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  ""


--gold-standard / -gold

Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison
Some analyses want to count overlap not with dbSNP (which is in general very open) but actually want to itemize their overlap specifically with a set of gold standard sites such as HapMap, OMNI, or the gold standard indels. This argument provides a mechanism for communicating which file to use

FeatureInput[VariantContext]  null


--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]  []


--keep-ac0 / -keep-ac0

If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes

boolean  false


--known-cnvs / -known-cnvs

File containing tribble-readable features describing a known list of copy number variants
File containing tribble-readable features containing known CNVs. For use with VariantSummary table.

FeatureInput[Feature]  null


--KNOWN_NAMES / -known-name

Name of feature bindings containing variant sites that should be treated as known when splitting eval features into known and novel subsets
List of feature tracks to be used for specifying "known" variants other than dbSNP.

HashSet[String]  []


--lenient / -LE

Lenient processing of VCF files

boolean  false


--list / -ls

List the available eval modules and exit
Note that the --list argument requires a fully resolved and correct command-line to work.

Boolean  false


--mendelian-violation-qual-threshold / -mvq

Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.

double  50.0  [ [ -∞  ∞ ] ]


--merge-evals / -merge-evals

If provided, all -eval tracks will be merged into a single eval track
If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying variant set, and evaluate the union of the results. Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.

boolean  false


--min-phase-quality / -mpq

Minimum phasing quality

double  10.0  [ [ -∞  ∞ ] ]


--output / -O

File to which variants should be written

R File  null


--pedigree / -ped

Pedigree file for determining the population "founders"

File  null


--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[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


--require-strict-allele-match / -strict

If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping

boolean  false


--sample / -sn

Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context

Set[String]  []


--sample-ploidy / -ploidy

Per-sample ploidy (number of chromosomes per sample)

int  2  [ [ -∞  ∞ ] ]


--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]


--SELECT_EXPS / -select

One or more stratifications to use when evaluating the data

ArrayList[String]  []


--SELECT_NAMES / -select-name

Names to use for the list of stratifications (must be a 1-to-1 mapping)

ArrayList[String]  []


--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


--strat-intervals / -strat-intervals

File containing tribble-readable features for the IntervalStratificiation
File containing tribble-readable features for the IntervalStratificiation

FeatureInput[Feature]  null


--stratification-module / -ST

One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)

List[String]  []


--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  null


--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


--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


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GATK version 4.1.2.0 built at Tue, 23 Apr 2019 14:55:55 -0400.