Skip to content

v0.17
Compare
Choose a tag to compare
@holtgrewe holtgrewe released this 17 Aug 15:09
· 701 commits to main since this release
v0.17
4fd8109

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.17.jar.

v0.17

jped-cli

  • this is gone, the functionality is now available as part of jannovar-cli

jannovar-filter

  • this module is done, everything here is merged into jannovar-htsjdk

jannovar-vardbs

  • The first version ships with support for dbSNP b147, ExAC 0.3, and the UK10K COHORT data base
  • Initial version of this module, the aim is precise annotation from variant databases

jannovar-cli

  • Updated default_sources.ini for latest patches of mouse and human genomes
  • Using one-letter amino acid code by default
  • Removed slf4j2 warning at program startup
  • Checking pedigree for compatibility with VCF file if given

jannovar-core

  • Adjusting API for annotating amino acid code by default
  • Checking pedigree for compatibility with genotypes on Mendelian inheritance checking
  • Refurbishing Genotype, GenotypeList, and GenotypeListBuilder in de.charite.compbio.jannovar.mendel.
  • Moving ModeOfInheritance to de.charite.compbio.jannovar.mendel.
  • Creating new package de.charite.compbio.jannovar.mendel with code for filtering for mendelian inheritance modes.
  • Renaming of ModeOfInheritance.UNINITIALIZED to ModeOfInheritance.ANY.
  • Fixing handling of invalid transcripts (e.g., incomplete 3' end)
  • Adding altGeneIDs mapping to TranscriptModel, makes data bases backwards incompatible.
  • Rewrite of GFF parsers for RefSeq and ENSEMBL.
  • Bumping HTSJDK to 2.5.0, requiring Java 8 from now on.
  • Removal of AnnotationCollector, priotization of variant effects is done after collecting all effect predictions now.
  • Fix for intronic variants between 5' or 3' UTRs. These variants were misclassified as FIVE_PRIME_UTR_VARIANT or THREE_PRIME_UTR_VARIANT. SequenceOntology implements new terms so that we can decide between the two UTR exon and intron variants. Now we have FIVE_PRIME_UTR_EXON_VARIANT or FIVE_PRIME_UTR_EXON_INTRON_VARIANT (the same for THREE_PRIME_UTR_EXON_VARIANT or THREE_PRIME_UTR_EXON_INTRON_VARIANT).

jannovar-cli

  • Adding better progress display with estimate of pending time.
  • Adding support for annotating values from dbSNP VCF file (currently, only b147 is supported).
  • Adding simple progress reporting (from verbosity level 2).
  • Using Java 8 stream interface for VariantContext processing.
  • Removing support for Jannovar output format, VCF offer all features and more.
Assets 2
Loading