holtgrewe
released this
overall
- Fixing
ANN
annotation field to have.
/unbound cardinality. - Bumping several dependencies, including HTSJDK.
manual
- Adding conda support in installation documentation
- Fixing broken link in quickstart
jannovar-core
- Fixing annotation of SVs that look like sequence variants (#456).
Interpretation is to use the sequence variant annotation code now.
This fixes a bug with annotating latest ClinVar for GRCh38. - Prevent
Annotation.{getPutativeImpact,getPutativeImpact}()
from returningnull
(#458). - Correctly parsing RefSeq mitochondrial transcripts.
Bumping the required versin to0.33-SNAPSHOT
to higlight this (#463).
Assets
2
overall
- Changing log4j version to 2.11.2
- Changing slf4j version to 1.7.25
jannovar-cli
- Adding a simple REST server for annotating single variants.
- Launch with
jannovar-cli rest-server -d data/hg19_refseq.ser -d data/hg19_ensembl.ser
- Then, query with
/annotate-var/refseq/hg19/chr7/140453136/A/T
or/annotate-var/ensembl/hg19/chr7/140453136/A/T
- Launch with
Assets
2
This release fixes an important issue with RefSeq transcripts that align with gaps to the genome (issues #447 #450). Overall 500 genes are affected including MYH7
! You probably want to upgrade to this release.
jannovar-core
- Introducing classes for representation of gapped sequences, alignments, and position projection.
- Fixing bug in ENSEMBL transcript database generation (tx version was appended twice)
- Adding flags for "has substitutions" and "has indels" to
TranscriptModel
that get filled for RefSeq transcripts. - Correctly parsing of RefSeq transcripts with indels.
jannovar-cli
Assets
2
Bugfix release.
jannovar-core
- Fixing interpretation of
INFO/SVTYPE
, urldecode and only use the first component after splitting at ":". - Interpreting SV type annotation for SV2 more correctly.
Assets
2
jannovar-core
- Putative impact of splice_region_variant has changed from MODERATE to LOW (see issue #439)
- Decreasing log verbosity in one location when building database.
- Fixing CDS region import in
RefSeqParser
- Putative impact of
splice_region_variant has
changed from MODERATE to LOW (see issue #439) - Fixing SV annotation using hg38/ucsc for transcripts without gene ID (see #444).
- Adding support for rn6 RefSeq transcripts.
AddingallowNonCodingNm
directive for data source INI file to disable check that RefSeq NM transcript has CDS. - Adding versions to ENST accessions for ENSEMBL.
jannovar-vardbs
- Bugfix: TSVAnnotator did not use end given column.
Assets
2
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 exceptionInvalidGenomeVariant
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.
Assets
2
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
Assets
2
jannovar-cli
- Making
OneParentGtFiltered
filter optional. The default setting tofalse
(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 theANN
field.
Assets
2
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