A Scala library extending ADAM and BDG-formats to load .vcf files annotated with SnpEff.

[WARNING: this library is still under heavy development. Expect versions to break compatibility.]

Artifacts are published to Bintray.

resolvers += "bintray-tmoerman" at "http://dl.bintray.com/tmoerman/maven"`

libraryDependencies += "org.tmoerman" %% "adam-fx" % "0.5.5"

:remote-repo bintray-tmoerman % default % http://dl.bintray.com/tmoerman/maven % maven

:dp org.tmoerman % adam-fx_2.10 % 0.5.5

%dep

z.addRepo("bintray-tmoerman").url("http://dl.bintray.com/tmoerman/maven")

z.load("org.tmoerman:adam-fx_2.10:0.5.5")

The AnnotatedVariant and AnnotatedGenotype classes are the "connector" types between the Adam types and the SnpEffAnnotations.

Class diagrams distilled from the Java classes generated from the Avro schema definition.

Adam-fx has its own KryoRegistrator that extends the ADAMKryoRegistrator with additional Avro data types. Use it when initializing a SparkConf.

val conf = new SparkConf()
    .setAppName("Test")
    .setMaster("local[*]")
    .set("spark.kryo.registrator", "org.tmoerman.adam.fx.serialization.AdamFxKryoRegistrator")
    .set("spark.kryo.referenceTracking", "true")
    .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
    
val sc = new SparkContext(conf)

Instantiate a SnpEffContext, passing it a SparkContext.

In a notebook setting you may want to use the @transient annotation in order to prevent serialization issues.

import org.tmoerman.adam.fx.snpeff.SnpEffContext

@transient val ec = new SnpEffContext(sc)

Or you could simply import the implicit conversions and use an (already instantiated) SparkContext reference.

import org.tmoerman.adam.fx.snpeff.SnpEffContext._

Loading Variants with SnpEffAnnotations:

val annotatedVariants: RDD[AnnotatedVariant] = sc.loadAnnotatedVariants(annotatedVcf)

Or Genotypes with SnpEffAnnotations:

val annotatedGenotypes: RDD[AnnotatedGenotype] = sc.loadAnnotatedGenotypes(annotatedVcf)