Field Detail

• 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:

  Constant Field Values

• REV_COMPED_ALLELES

  public static final String REV_COMPED_ALLELES

  See Also:

  Constant Field Values

• 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 Detail

• LiftoverUtils

  public LiftoverUtils()

Method Detail

• 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)

  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

  Returns:

  The lifted VariantContext. This will be null if the input VariantContext could not be lifted.

• 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

• referenceAlleleMatchesReferenceForIndel

  protected static boolean referenceAlleleMatchesReferenceForIndel​(List<htsjdk.variant.variantcontext.Allele> alleles,
                                                                   htsjdk.samtools.reference.ReferenceSequence referenceSequence,
                                                                   int start,
                                                                   int end)

  Checks whether the reference allele in the provided variant context actually matches the reference sequence

  Parameters:

  alleles - list of alleles from which to find the reference allele

  referenceSequence - the ref sequence

  start - the start position of the actual indel

  end - the end position of the actual indel

  Returns:

  true if they match, false otherwise

• 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, G. R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.