charite/jannovar

Issues

• Exception in thread "main" java.lang.NullPointerException

  #567 opened a year ago by leemdi
  1

• Rest Server Error: Bad Message 414 reason: URI Too Long

  #561 opened a year ago by janeliutw
  0

• Command download broken

  #550 opened 3 years ago by holtgrewe
  1

• Update ini4j dependency to at least 0.5.4 due to CVE-2022-41404

  #566 opened 2 years ago by thomasredlin
  0

• UTF-8 output for synonymous mutations in VCF file

  #560 opened 2 years ago by skurscheid
  1

• Jannovar does not annotate deletions for stop_gained (only frameshift)

  #557 opened 2 years ago by janeliutw
  2

• Dragen CNV output cannot be parsed

  #558 opened 2 years ago by holtgrewe
  0

• Insertions are not annotated for splicing

  #554 opened 2 years ago by dmb107
  3

• 3' Shifting

  #551 opened 3 years ago by lshimp
  11

• Meaning of --no-3-prime-shifting is inverted

  #552 opened 2 years ago by holtgrewe
  0

• Enhancements to hgvs to vcf conversion resiliency

  #549 opened 3 years ago by h-joshi
  0

• Code optimization suggestions

  #548 opened 3 years ago by noobyu6
  0

• Support MANE transcripts

  #546 opened 3 years ago by holtgrewe
  0

• Invalid aminoacid change detected due to GTF file phase ignored

  #541 opened 3 years ago by znikasz
  2

• Problem of HGVSc conversion

  #532 opened 3 years ago by smw1414
  1

• hgvs-to-vcf hanging when encountering incorrect hgvs entries

  #539 opened 3 years ago by h-joshi
  1

• Building hg38/ensembl version 105 results in NPE

  #540 opened 3 years ago by znikasz
  0

• broken links to datasets download

  #533 opened 3 years ago by myeelaw
  2

• mitochondrial genetic code

  #501 opened 3 years ago by smw1414
  1

• Use single branch instead of develop/master split.

  #521 opened 4 years ago by holtgrewe
  2

• Getting java.lang.InternalError while annotation with 1000 Genome Db

  #480 opened 5 years ago by Habush
  0

• RefSeq datasets for mm11

  #531 opened 3 years ago by myeelaw
  7

• Complete support for parsing HGVS nucleotide expressions.

  #519 opened 4 years ago by holtgrewe
  5

• Report the effect for every genes

  #530 opened 4 years ago by smw1414
  1

• HGVS-VCF bug ( de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant: No transcript )

  #529 opened 4 years ago by mansi800
  1

• Remove support for UCSC transcripts

  #523 opened 4 years ago by holtgrewe
  5

• unable to download Mouse transcript databases

  #492 opened 4 years ago by myeelaw
  1

• Error while trying to download human hg-19 reference using jannovar v 0.34 installed via bioconda

  #495 opened 4 years ago by guglusharma
  7

• Refurbish vardbs/frequency annotation

  #511 opened 4 years ago by holtgrewe
  1

• Building ReferenceDictionary fails for hg19/*

  #486 opened 4 years ago by stolpeo
  16

• `default_sources.ini` seems not to cover all download links

  #489 opened 4 years ago by stolpeo
  0

• Error with chr_accessions_GRCh38.p12

  #497 opened 4 years ago by pnrobinson
  0

• NCBI urls are out-of-date

  #500 opened 4 years ago by phwhite-coh
  5

• Deposit static files into Zenodo

  #513 opened 4 years ago by holtgrewe
  8

• Problems with projection of dbSNP variants and RefSeq for hg38

  #524 opened 4 years ago by holtgrewe
  2

• JUNIT 5

  #505 opened 4 years ago by pnrobinson
  5

• ERROR: [ERROR] Input string for the chromosomal change

  #482 opened 4 years ago by zillurbmb51
  1

• Translation of HGVS into VCF stalls when writing VCF file with some mutations

  #483 opened 4 years ago by mmcneill123
  4

• Implement HGVS parsing for protein sequences

  #516 opened 4 years ago by holtgrewe
  0

• Cannot parse HGVS repeats

  #490 opened 5 years ago by markwoon
  1

• Problem parsing HGVS `delins`

  #491 opened 4 years ago by markwoon
  2

• Cannot parse HGVS `NP_000095.2:p.Gly168_His169=`

  #493 opened 4 years ago by markwoon
  3

• Remove INI support for hg18

  #504 opened 4 years ago by pnrobinson
  0

• HGVS protein annotation error for deletions (may impact other mutation types e.g. ins)

  #481 opened 4 years ago by wmgmm
  1

• Faulty right-shifting of deletions for protein annotations

  #498 opened 4 years ago by roland-ewald
  0

• --show-all option not properly worked

  #503 opened 4 years ago by smw1414
  2

• Step by step procedure

  #496 opened 4 years ago by KarthickRajaNarayanan
  4

• Download/processing of hg19/* fails

  #487 opened 5 years ago by stolpeo
  1

• -d hg38/refseq not found

  #484 opened 5 years ago by pnrobinson
  1

• String index out of bounds for variant GRCh37 `chr11:67258349AGCTGGACCCAGCC>GT`

  #475 opened 5 years ago by ielis
  3