Package picard.util

Class LiftoverUtils

java.lang.Object
picard.util.LiftoverUtils

public class LiftoverUtils extends Object
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final Collection<String>
     
    static final Collection<String>
    Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
    static final htsjdk.samtools.util.Log
     
    static final String
     
    static final String
    Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    protected static List<String>
    allelesToStringList(List<htsjdk.variant.variantcontext.Allele> alleles)
    This is a utility method that will convert a list of alleles into a list of base strings.
    protected static htsjdk.variant.variantcontext.GenotypesContext
    fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals, List<htsjdk.variant.variantcontext.Allele> originalAlleles, List<htsjdk.variant.variantcontext.Allele> newAlleles)
     
    protected static void
    leftAlignVariant(htsjdk.variant.variantcontext.VariantContextBuilder builder, int start, int end, List<htsjdk.variant.variantcontext.Allele> alleles, htsjdk.samtools.reference.ReferenceSequence referenceSequence)
    Normalizes and left aligns a VariantContextBuilder.
    protected static htsjdk.variant.variantcontext.VariantContextBuilder
    liftSimpleVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target)
     
    static htsjdk.variant.variantcontext.VariantContext
    liftVariant(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq, boolean writeOriginalPosition, boolean writeOriginalAlleles)
    This will take an input VariantContext and lift to the provided interval.
    protected static htsjdk.variant.variantcontext.VariantContextBuilder
    reverseComplementVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq)
     
    static htsjdk.variant.variantcontext.VariantContext
    swapRefAlt(htsjdk.variant.variantcontext.VariantContext vc, Collection<String> annotationsToReverse, Collection<String> annotationsToDrop)
    method to swap the reference and alt alleles of a bi-allelic, SNP

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • SWAPPED_ALLELES

      public static final String SWAPPED_ALLELES
      Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
      See Also:
    • REV_COMPED_ALLELES

      public static final String REV_COMPED_ALLELES
      See Also:
    • DEFAULT_TAGS_TO_REVERSE

      public static final Collection<String> DEFAULT_TAGS_TO_REVERSE
      Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
    • DEFAULT_TAGS_TO_DROP

      public static final Collection<String> DEFAULT_TAGS_TO_DROP
    • log

      public static final htsjdk.samtools.util.Log log
  • Constructor Details

    • LiftoverUtils

      public LiftoverUtils()
  • Method Details

    • liftVariant

      public static htsjdk.variant.variantcontext.VariantContext liftVariant(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq, boolean writeOriginalPosition, boolean writeOriginalAlleles)
      This will take an input VariantContext and lift to the provided interval. If this interval is in the opposite orientation, all alleles and genotypes will be reverse complemented and indels will be left-aligned. Currently this is only able to invert biallelic indels, and null will be returned for any unsupported VC.
      Parameters:
      source - The VariantContext to lift
      target - The target interval
      refSeq - The reference sequence, which should match the target interval
      writeOriginalPosition - If true, INFO field annotations will be added to store the original position and contig
      writeOriginalAlleles - If true, an INFO field annotation will be added to store the original alleles in order. This can be useful in the case of more complex liftovers, like reverse complements, left aligned indels or swapped REF/ALT
      Returns:
      The lifted VariantContext. This will be null if the input VariantContext could not be lifted.
    • allelesToStringList

      protected static List<String> allelesToStringList(List<htsjdk.variant.variantcontext.Allele> alleles)
      This is a utility method that will convert a list of alleles into a list of base strings. Reference status is ignored when creating these strings (i.e. 'A', not 'A*'). These strings should be sufficient to recreate an Allele using Allele.create()
      Parameters:
      alleles - The list of alleles
      Returns:
      A list of strings representing the bases of the input alleles.
    • liftSimpleVariantContext

      protected static htsjdk.variant.variantcontext.VariantContextBuilder liftSimpleVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target)
    • reverseComplementVariantContext

      protected static htsjdk.variant.variantcontext.VariantContextBuilder reverseComplementVariantContext(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target, htsjdk.samtools.reference.ReferenceSequence refSeq)
    • fixGenotypes

      protected static htsjdk.variant.variantcontext.GenotypesContext fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals, List<htsjdk.variant.variantcontext.Allele> originalAlleles, List<htsjdk.variant.variantcontext.Allele> newAlleles)
    • swapRefAlt

      public static htsjdk.variant.variantcontext.VariantContext swapRefAlt(htsjdk.variant.variantcontext.VariantContext vc, Collection<String> annotationsToReverse, Collection<String> annotationsToDrop)
      method to swap the reference and alt alleles of a bi-allelic, SNP
      Parameters:
      vc - the VariantContext (bi-allelic SNP) that needs to have it's REF and ALT alleles swapped.
      annotationsToReverse - INFO field annotations (of double value) that will be reversed (x->1-x)
      annotationsToDrop - INFO field annotations that will be dropped from the result since they are invalid when REF and ALT are swapped
      Returns:
      a new VariantContext with alleles swapped, INFO fields modified and in the genotypes, GT, AD and PL corrected appropriately
    • leftAlignVariant

      protected static void leftAlignVariant(htsjdk.variant.variantcontext.VariantContextBuilder builder, int start, int end, List<htsjdk.variant.variantcontext.Allele> alleles, htsjdk.samtools.reference.ReferenceSequence referenceSequence)
      Normalizes and left aligns a VariantContextBuilder. Note: this will modify the start/stop and alleles of this builder. Also note: if the reference allele does not match the reference sequence, this method will throw an exception Based on Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.