Package org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging

Class SimpleGermlineTagger

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.SimpleGermlineTagger

public class SimpleGermlineTagger
extends Object

This utility class performs a simple tagging of germline segments in a tumor segments file.

Method Summary

Modifier and Type	Method	Description
static List<AnnotatedInterval>	tagTumorSegmentsWithGermlineActivity(List<AnnotatedInterval> initialTumorSegments, List<AnnotatedInterval> initialNormalSegments, String callAnnotation, htsjdk.samtools.SAMSequenceDictionary dictionary, String outputAnnotationName, int paddingInBp, double reciprocalThreshold)	Look for concordant endpoints for determining whether an event in the tumor regions are in the germline regions.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

tagTumorSegmentsWithGermlineActivity

public static List<AnnotatedInterval> tagTumorSegmentsWithGermlineActivity(List<AnnotatedInterval> initialTumorSegments,
 List<AnnotatedInterval> initialNormalSegments,
 String callAnnotation,
 htsjdk.samtools.SAMSequenceDictionary dictionary,
 String outputAnnotationName,
 int paddingInBp,
 double reciprocalThreshold)

Look for concordant endpoints for determining whether an event in the tumor regions are in the germline regions. This method will not modify the input segments.

Parameters:

initialTumorSegments - segment file from the tumor sample. Cannot contain intervals that overlap. Must have calls that are using the annotation from the parameter callAnnotation. No calls can be the empty string. Never null.

initialNormalSegments - segment file from the normal sample. Must have calls that are using the annotation from the parameter callAnnotation. No calls can be the empty string. Cannot contain intervals that overlap. Never null.

callAnnotation - the annotation name (e.g. "CALL") used in both the tumor and normal segment files. Never null.

dictionary - sequence dictionary used to generate the segment files. Used for sorting. Never null.

outputAnnotationName - annotation to append to the tumor segments. If you specify one that exists, it will overwrite. Cannot be null nor empty string.

paddingInBp - The amount of slop to give (in bp) for matching segment endpoints. Must be >= 0

reciprocalThreshold - The reciprocal threshold between the normal and tumor segment that must match in order to match (whether or not matching breakpoints are found). Must be 0.0 to 1.0.

Returns:

copy of the tumor segments (sorted) with the additional germline tag annotation (the name of which is outputAnnotationName).