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# What are JEXL expressions and how can I use them with the GATK?

edited December 8 in FAQs

### 1. JEXL in a nutshell

JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for many things, but in the context of the GATK, it has one very specific use: making it possible to operate on subsets of variants from VCF files based on one or more annotations, using a single command. This is typically done with walkers such as VariantFiltration and SelectVariants.

### 2. Basic structure of JEXL expressions for use with the GATK

In this context, a JEXL expression is a string (in the computing sense, i.e. a series of characters) that tells the GATK which annotations to look at and what selection rules to apply.

JEXL expressions contain three basic components: keys and values, connected by operators. For example, in this simple JEXL expression which selects variants whose quality score is greater than 30:

"QUAL > 30.0"

• QUAL is a key: the name of the annotation we want to look at
• 30.0 is a value: the threshold that we want to use to evaluate variant quality against
• > is an operator: it determines which "side" of the threshold we want to select

The complete expression must be framed by double quotes. Within this, keys are strings (typically written in uppercase or CamelCase), and values can be either strings, numbers or booleans (TRUE or FALSE) -- but if they are strings the values must be framed by single quotes, as in the following example:

"MY_STRING_KEY == 'foo'"


### 3. Evaluation on multiple annotations

You can build expressions that calculate a metric based on two separate annotations, for example if you want to select variants for which quality (QUAL) divided by depth of coverage (DP) is below a certain threshold value:

"QUAL / DP < 10.0"


You can also join multiple conditional statements with logical operators, for example if you want to select variants that have both sufficient quality (QUAL) and a certain depth of coverage (DP):

"QUAL > 30.0 && DP == 10"


where && is the logical "AND".

Or if you want to select variants that have at least one of several conditions fulfilled:

"QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0"


where || is the logical "OR".

### 4. Important caveats

#### Sensitivity to case and type

• Case

Currently, VCF INFO field keys are case-sensitive. That means that if you have a QUAL field in uppercase in your VCF record, the system will not recognize it if you write it differently (Qual, qual or whatever) in your JEXL expression.

• Type

The types (i.e. string, integer, non-integer or boolean) used in your expression must be exactly the same as that of the value you are trying to evaluate. In other words, if you have a QUAL field with non-integer values (e.g. 45.3) and your filter expression is written as an integer (e.g. "QUAL < 50"), the system will throw a hissy fit (aka a Java exception).

#### Complex queries

We highly recommend that complex expressions involving multiple AND/OR operations be split up into separate expressions whenever possible to avoid confusion. If you are using complex expressions, make sure to test them on a panel of different sites with several combinations of yes/no criteria.

### 5. More complex JEXL magic

Note that this last part is fairly advanced and not for the faint of heart. To be frank, it's also explained rather more briefly than the topic deserves. But if there's enough demand for this level of usage (click the "view in forum" link and leave a comment) we'll consider producing a full-length tutorial.

#### Introducing the VariantContext object

When you use SelectVariants with JEXL, what happens under the hood is that the program accesses something called the VariantContext, which is a representation of the variant call with all its annotation information. The VariantContext is technically not part of GATK; it's part of the variant library included within the Picard tools source code, which GATK uses for convenience.

The reason we're telling you about this is that you can actually make more complex queries than what the GATK offers convenience functions for, provided you're willing to do a little digging into the VariantContext methods. This will allow you to leverage the full range of capabilities of the underlying objects from the command line.

In a nutshell, the VariantContext is available through the vc variable, and you just need to add method calls to that variable in your command line. The bets way to find out what methods are available is to read the VariantContext documentation on the Picard tools source code repository (on SourceForge), but we list a few examples below to whet your appetite.

#### Examples using VariantContext directly

For example, suppose I want to use SelectVariants to select all of the sites where sample NA12878 is homozygous-reference. This can be accomplished by assessing the underlying VariantContext as follows:

java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.getGenotype("NA12878").isHomRef()'


Groovy, right? Now here's a more sophisticated example of JEXL expression that finds all novel variants in the total set with allele frequency > 0.25 but not 1, is not filtered, and is non-reference in 01-0263 sample:

! vc.getGenotype("01-0263").isHomRef() && (vc.getID() == null || vc.getID().equals(".")) && AF > 0.25 && AF < 1.0 && vc.isNotFiltered() && vc.isSNP() -o 01-0263.high_freq_novels.vcf -sn 01-0263


#### Examples using the VariantContext to evaluate boolean values

The classic way of evaluating a boolean goes like this:

java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R b37/human_g1k_v37.fasta --variant my.vcf -select 'DB'


But you can also use the VariantContext object like this:

java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.hasAttribute("DB")'


#### Example using JEXL to evaluate arrays

Sometimes you might want to write a JEXL expression to evaluate e.g. the AD (allelic depth) field in the FORMAT column. However, the AD is technically not an integer; rather it is a list (array) of integers. One can evaluate the array data using the "." operator. Here's an example:

java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.getGenotype("NA12878").getAD().0 > 10'

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Tagged:

Geraldine Van der Auwera, PhD

• chinaPosts: 3Member

Hi Geraldine_VdAuwera, Thanks for the detail about JEXL expression .I used SelectVariants -select 'vc.getGenotype("SampleN").isHet' or .isHomVar for selecting the known genotype like "0/1 or 1/1". But in my VCF file, there are some missing genotype like "." , and I also want to select those unknow genotype. Can you give me some comments for this. Thanks.

Best, Xie

Hi Xie,

To select the unknown genotypes (./.) you can select for anything that is not homref, het, or homvar.

-Sheila

• chinaPosts: 3Member

Hi Sheila, thank you for you timely reply. I select by vc.getGenotype('sample08').isnotHomVar() ..., but there is error: "Invalid JEXL expression detected for select-0 with message ![72,85]: vc.getGenotype('sample08').isnotHomVar() && vc.getGenotype('sample08').isnotHet();' unknown, ambiguous or inaccessible method isnotHomVar" I think the problem is incorrect JEXL expression. So are there some JEXL expressions for select setting ? Thanks, Xie

Hi Xie,

Instead of using vc.getGenotype('sample08').isnotHomVar(), try using ! vc.getGenotype('sample08').isHomVar(). The ! means not.

-Sheila

• chinaPosts: 3Member