de.charite.compbio.jannovar.vardbs.base

Interface DBAnnotationDriver

All Known Implementing Classes:

AbstractDBAnnotationDriver, DBSNPAnnotationDriver, ExacAnnotationDriver, UK10KAnnotationDriver

public interface DBAnnotationDriver

Interface for annotation drivers by variant databases.

Author:

Manuel Holtgrewe

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.variantcontext.VariantContext	annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc) Annotate the VariantContext object using the information in the database.
VCFHeaderExtender	constructVCFHeaderExtender()

Method Detail

constructVCFHeaderExtender

VCFHeaderExtender constructVCFHeaderExtender()

Returns:

The VCFHeaderExtender to use.

annotateVariantContext

htsjdk.variant.variantcontext.VariantContext annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)

Annotate the VariantContext object using the information in the database. Note that the annotation in jannovar-vardbs makes a distinction between variants that are in the database and variants that are only at the same position or overlap.

Parameters:

vc - VariantContext to annotate

Returns:

Updated VariantContext object