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v0.21
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@holtgrewe holtgrewe released this 04 Apr 08:36
· 477 commits to main since this release
v0.21
fee27d8

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.21.jar.

all

  • Fixing language in mvn surfire plugin. Now mvn tests work on locale de_DE etc..

jannovar-cli

  • Adding --interval argument for only processing a part of the file
  • Adding statistics command for computing statistics on variants in VCF file
  • Fixing bug in HGVS to VCF
  • Better handling missing .dict file for HGVS to VCF translation
  • Adding --annotate-as-singleton-pedigree parameter for annotation of singleton pedigrees without pedigree file (single individual is assumed to be affected)
  • More friendly user message in case of unsorted files on inheritance mode annotation
  • Interpretation of filters in compatible inheritance mode annotation
  • Integrating new jannovar-filter into Jannovar CLI.
    Filtered genotypes will be passed into the inheritance filter as no-call.
  • Adding annotation with ClinVar
  • Printing warnings next to the annotations in annotate-pos
  • AR inheritance annotation of two siblings bugfix (no parents avaiable in comp.het mode) #314

jannovar-filter

  • Adding functionality to add filters based on frequencies found in dbSNP and ExAC
  • Adding back as module for threshold-based filtration.
    This module allows to create genotype-wise soft-filters for low coverage.
    Also, variants can be soft-filtered based on whether the genotype calls of all affected individuals are filtered out.

jannovar-core

  • Extending API to expose mendelian checks for comp het./ad alt (via SubModuleOfInheritance and MendelianInheritanceChecker
  • Jannovar version is now written out to database file which allows better error checks and compatibility messages
  • Un-deprecating BestAnnotationListTextGenerator and AllAnnotationListTextGenerator classes, useful for text-based output formats
  • Changing behaviour of VariantEffect.isOffExome() and adding a variant that allows to decide between UTR on/off exome and non-consensus splice region on/off exome
  • Making the behaviour of overriding transcripts configurable at least in the code, using default to not do this any more
  • Adding WARNING_REF_DOES_NOT_MATCH_TRANSCRIPT to AnnotationMessage
  • Properly pushing through warnings from the annotators into the returned VariantAnnotation object
  • Pedigree files are now more compatible to the PLINK format
    • whitespace separated instead of tab separated (read only, written as TSV)
    • interpreting any value not in {1, 2} to be "unknown" sex instead (coded as 0) of throwing

jannovar-htsjdk

  • Fixing bug in transcript-to-genome translation, in HGVS the stop codon is not part of the CDS but in TranscriptModel it is
  • Optional interpretation of certain filters in GeneWiseMendelianAnnotationProcessor.
  • Extending interface of VariantContextAnnotator for automatic error annotation generation, previously in jannovar-cli
  • Adding VariantEffectHeaderExtender class to jannovar-htsjdk
  • Fixing bug with problems of unmodifiable Attributes (error annotation).

jannovar-vardbs

  • Also writing out variant allele origin for dbSNP
  • Adding annotation with COSMIC
  • Fixing header description for exac database
  • Fixing output of DBSNP_CAF to also contain reference allele AF
  • Adding annotation with ClinVar, can annotate all clinvar variants

jannovar-inheritance-checker

  • Removing this outdated module.
    Use the classes in de.charite.compbio.jannovar.mendel instead

jannovar-stats

  • all-new module for gathering statistics on VCF files
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