v0.28

jannovar-cli

• Bumping ENSEMBL versions for GRCh37 and GRCh38.
• Fixing sources information for updated ENSEMBL downloads.
• For ENSEMBL, use ENSEMBL-provided mapping from ENSG to HGNC ID for Entrez ID assignment.
  This is necessary as Ensembl gene IDs turn out to be not so stable between hg37 and hg38 after all.
  Case in point: ENSG00000276141 vs. ENSG00000187667.
• Adding --gene-ids argument to downloader for creating smaller databases (mostly for test purposes).
• Adding SV support to jannovar-cli, includes tests.
• Using ENSEMBL-provided mapping from ENSG to Entrez ID in the case HGNC mapping does not work.

jannovar-htsjdk

• Adding SV support to jannovar-htsjdk
• Bumping HTSJDK dependency to v2.18.2

jannovar-core

• Changing upstream/downstream size to 5kbp.
• Support for prioritizing RefSeq transcript on the PAR of chrX over those of chrY
• Refactorizations to improve performace using EnumSet.
• Extended VariantEffect for the effects of structural variants.
  Removing documentation that the effect is not used in Jannovar for some now interpreted ones.
  Also variant effect for non-coding variants is added using the current VEP predictions as a template.
• Prohibiting creating GenomeVariant with symbolic alleles.
  Throwing new checked exception InvalidGenomeVariant case of error.
• Fixing SO term ID for VariantEffect.DISRUPTIVE_INFRAME_DELETION
• Correctly parsing transcript version for ENSEMBL when available (not available for b75/GRCh37).
• Making transcript model building (for download) more memory efficient.

v0.27

jannovar-cli

• Integrating support for thousand genomes VCF
• Integrating thousand genomes/ExAc count limits into inheritance filter

jannovar-vardbs

• Adding support for thousand genomes VCF

jannovar-htsjdk

• Adding support for limiting genomes/ExAc counts into inheritance filter

v0.26

jannovar-cli

• Making OneParentGtFiltered filter optional. The default setting to false (specify --one-parent-gt-filtered-filters-affected to enable).

jannovar-core

• Moving variants in non-coding transcripts after UTR variants.

jannovar-hgvs

• Fixing parser issue for nucleotide indels (#408).

jannovar-htsjdk

• Obey the options.escapeAnnField parameter for escaping the variant effect in the ANN field.

v0.25

As in all recent releases, Jannovar is best installed through Maven Central.

overall

• Changing HTSJDK version to 2.14.3
• Using the one letter amino acid code in HGVS representation as default (changes in core, hgvs, htsjdk and cli). Now the cli option --3-letter-amino-acids works as expected.

jannovar-cli

• Support for RefSeq GRCh37.p13 interim release
• Support of new RefSeq headers
• Using RefSeq GRCh38.p12 annotation instead of GRCh38.p7

jannovar-vardbs

• Replacing whitespace with string when annotating from TSV file.

jannovar-htsjdk

• Fixing bug in GenomeRegionSequenceExtraction. Error reports always sequences from the first contig in the referebnce file and not the requested contig. Affects only the cli command hgvs-to-vcf.

v0.24

overall

• Changing HTSJDK version to 2.14.0
• Codestyle approvements

jannovar-cli

• Fixing annotation with Polyphen prediction (data type)

jannovar-core

• Fixing mendelian "bug" #393 (has no affect because check was not necessary)
• New inheritance mode: mitochondrial
• Bugfix ProgressBar (doPrint was always true)

jannovar-vardbs

• Fixed problem with interpretation of Clinvar annotation origin.
• Clinvar BEST_AC and BEST_AF are now named AC_POPMAX and AF_POPMAX to be consitent with gnomAD

v0.23

overall

• Changing Guava version to 0.22
• Changing slf4j version to 1.7.24
• Changing log4j version to 2.8.2

jannovar-cli

• Adding experimental support for annotating with VCF files.
• Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP.
• Integrating the advanced pedigree-based filters (useful for filtration to de novo variants).
• Making it possible to override database INI settings using user-specified INI files.

jannovar-core

• Fixing stop loss annotation (#351).
• Finishing renaming of TranscriptInfo to TranscriptModel (#348).
• Upstream and downstream variant were considered "not off exome". They now are.

jannovar-filter

• Adding code for performing more advanced filtration/annotation filtering to de novo variants.
• Improving documentation of MaxFreqAr and MaxFreqAd in header.

jannovar-vardbs

• Adding experimental support for annotating with VCF files
• Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP

jannovar-filter

• Fixing bug that ignored variant filters for recessive annotation

v0.22

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.22.jar.

jannovar-htsjdk

• Fixin NPE problem with inheritance annotation

jannovar-statistics

• Also counting number of variants on contigs
• Fixing counting bug that made UTR3 variants be counted as UTR5
• Fixing NPE in case of null variant annotations (e.g., unknown contig)

jannovar-vardbs

• Fixing a problem with normalization on variant annotation
• Fixing problem with default value of CLNSIG ("25" -> "255")

jannovar-filter

• Incorporating gnomAD annotation into exclusion by frequency for inheritance filter (#343)
• Fixing header description for MinAafHomAlt and MaxAafHomRef (#342)

jannovar-cli

• Checking that reference is given also for gnomAD VCF annotation

v0.21

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

v0.20

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.20.jar.

all

• Change email/organisations in master pom

jannovar-core

• GenotypeCalls.getGenotypeForSample() returns a "no-call" genotype now instead of null

jannovar-htsjdk

• fix to annotation with compatible mode of inheritance (#289)
• update to htsjdk 2.8.1

jannovar-cli

• removing requirement for proper contig contig lines in gene-wise gene annotation
• fixing NPE in the case of no contig lines
• improving error message on samples in VCF file that are not in pedigree
• fix to annotation with compatible mode of inheritance (#289)
• better overview on CLI help message
• if ref-fasta is not set properly a nicer error message will be shown.

jannovar-vardbs

• Fixing bug with problems of unmodifieable Attributes.
• Including Hom/Het/Hemi counds of ExAC (#295)
• update to htsjdk 2.8.1

v0.19

This is a bugfix release.

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.19.jar.

manual

• Manual loads version from central POM file now
• Adjusting manual links to point to javadoc.io

jannovar-core

• Fixing integration of HGNC into the downloaded databases
  • For UCSC, HGNC records are searched based on the Entrez ID.
    If HGNC does not know the Entrez then only the Entrez ID from UCSC is written as additional ID.
  • For RefSeq, linking is done through Entrez ID.
    If HGNC does not know the Entrez then only the Entrez ID from RefSeq is written as additional ID.
  • For ENSEMBL linking is done through the ENSEMBL gene id.
    If this is not known to HGNC then no additional IDs are annotated.
• Fixing problem with UnsupportedOperationException in jannovar-htsjdk