Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / pcingola/SnpEff issues and pull requests

#532 - HGVS Nomenclature issues

Issue - State: open - Opened by RaquelRomeroF 10 months ago

#531 - Incorrect classification duplication variant as intron coding?

Issue - State: open - Opened by kzaslavsky 10 months ago - 1 comment

#528 - Error: Unknown option '-noCheckCds'

Issue - State: open - Opened by tania-k 10 months ago

#527 - Protein fasta

Pull Request - State: closed - Opened by pcingola 10 months ago

#526 - Problem with downlading genome

Issue - State: closed - Opened by javierAPC 10 months ago

#524 - WISH: Version-specific download links

Issue - State: open - Opened by HenrikBengtsson 11 months ago

#523 - Make building and using a custom database easier.

Issue - State: open - Opened by J-Moravec 11 months ago

#522 - Database request: raccoon (Procyon lotor)

Issue - State: open - Opened by Joannakolodz 11 months ago

#519 - problems with building database for CriGri1.0

Issue - State: open - Opened by gabrielet 11 months ago

#517 - Different output when using -FileList

Issue - State: open - Opened by pcoenen 12 months ago

#514 - .genome not found

Issue - State: open - Opened by C37H41N2O6 about 1 year ago - 4 comments

#512 - Security Vulnerability

Issue - State: open - Opened by mohitmathew about 1 year ago

#511 - i was working on Variant Annotation ...the error was genes.gff not found

Issue - State: open - Opened by singha30 about 1 year ago - 2 comments

#510 - Another snpEff regression between versions 5.0 and 5.1/5.2

Issue - State: closed - Opened by tillea about 1 year ago - 2 comments

#506 - Why bacteria genome has predicted intron/exon regions?

Issue - State: closed - Opened by elifozcelik over 1 year ago - 2 comments

#502 - Fix typo in running.md

Pull Request - State: closed - Opened by tayabsoomro over 1 year ago - 1 comment

#501 - Unable to download GRCh38.mane.1.2.refseq: "The specified blob does not exist"

Issue - State: closed - Opened by jamigo over 1 year ago - 11 comments

#489 - Allele does not match allele in VCF

Issue - State: closed - Opened by bensprung over 1 year ago - 1 comment

#488 - Change Log?

Issue - State: closed - Opened by schorlton over 1 year ago - 3 comments

#486 - RUN snpEff-unable to access jarfile snpEff.jar

Issue - State: closed - Opened by Ligerd5 over 1 year ago - 1 comment

#483 - Potential LOF mutation being annotated as intergenic variant

Issue - State: closed - Opened by bvaditi over 1 year ago - 4 comments

#482 - FATAL ERROR: No CDS checked.

Issue - State: closed - Opened by selasphoruskershaw over 1 year ago - 2 comments

#481 - Build tests are failing in Eclipse

Issue - State: closed - Opened by JohnZaharick over 1 year ago - 1 comment

#476 - LoF and NMD annotations in SnpEFF (COVID version on Galaxy)

Issue - State: closed - Opened by ubakry almost 2 years ago - 1 comment

#474 - ann.vcf 'INFO' columns contain true variant then lots of additional information

Issue - State: closed - Opened by CSmith950 almost 2 years ago - 1 comment

#468 - New User, Novel Genome, Lots of WARNINGS, advise?

Issue - State: closed - Opened by robertwhbaldwin almost 2 years ago - 1 comment

#466 - Custom Database support

Issue - State: closed - Opened by Gon1976 almost 2 years ago

#465 - So term list using in SnpEff

Issue - State: closed - Opened by mentorlg almost 2 years ago

#464 - Error downloading E. coli database

Issue - State: closed - Opened by alexwong1357 almost 2 years ago - 1 comment

#462 - Header not updated in empty VCF

Issue - State: closed - Opened by r-blanchet almost 2 years ago

#459 - Customized gff3 file CDScheck error: CDSs do not match for transcript

Issue - State: closed - Opened by xiluo156 almost 2 years ago - 1 comment

#458 - Question about the Database

Issue - State: closed - Opened by dlwjd9659 about 2 years ago

#457 - Install snpEFF issue

Issue - State: closed - Opened by medbenamine about 2 years ago - 1 comment

#456 - Hg38 patch 13 compatibility

Issue - State: closed - Opened by 00username about 2 years ago

#455 - snpEff regression between versions 5.0 and 5.1

Issue - State: closed - Opened by pgrt about 2 years ago - 10 comments

#454 - Request for Database: Fall Armyworm

Issue - State: closed - Opened by MattHuff about 2 years ago

#451 - Sourceforge database links are down??

Issue - State: closed - Opened by hans-vg about 2 years ago - 2 comments

#449 - interpreting an annotation

Issue - State: closed - Opened by prasundutta87 about 2 years ago

#447 - Many annotation from one variant, which is the right one?

Issue - State: closed - Opened by manburst about 2 years ago

#446 - How can I resolve this error

Issue - State: closed - Opened by MuhammadSarfrazAli about 2 years ago

#445 - asking for the Database of Human gammaherpesvirus 4

Issue - State: closed - Opened by tongyt1225 about 2 years ago

#444 - can not find pre built database

Issue - State: closed - Opened by wantingwei about 2 years ago - 3 comments

#442 - Unable to start running snpEff

Issue - State: closed - Opened by HHLA917A about 2 years ago

#440 - Failure to download database

Issue - State: closed - Opened by amandahaponski about 2 years ago - 6 comments

#439 - Tagged distfiles?

Issue - State: closed - Opened by outpaddling about 2 years ago

#438 - SnpEff and SnpSift 5.1d do not seem to support multi-threading

Issue - State: closed - Opened by robertzeibich about 2 years ago - 1 comment

#435 - pb with p.HGVS indel annotation

Issue - State: closed - Opened by tomSimonet about 2 years ago - 2 comments

#433 - vulnerability issue in latest SnpeEff.jar

Issue - State: closed - Opened by yujun2017 over 2 years ago

#431 - Obviously the hg

Issue - State: closed - Opened by dfc-1931475 over 2 years ago - 1 comment

#423 - Invalid HGVSc annotation question

Issue - State: closed - Opened by seoung-chul over 2 years ago - 5 comments

#421 - Add COSMIC Annotation for Structural Variants

Issue - State: closed - Opened by nbarkas-az over 2 years ago

#420 - -fastaProt doesn't write a file when -t threading is specified

Issue - State: closed - Opened by liliblu over 2 years ago

#419 - building database with new genbank file format

Issue - State: closed - Opened by neve-b over 2 years ago

#417 - FATAL ERROR: No CDS checked

Issue - State: closed - Opened by hmoral over 2 years ago - 3 comments

#409 - Long HGVS frameshift nomenclature

Issue - State: closed - Opened by vyx-nir-neerman over 2 years ago - 1 comment

#408 - T2T-CHM13_v2.0 request

Issue - State: closed - Opened by 21tesla over 2 years ago - 2 comments

#401 - running -fastaProt + -fileList

Issue - State: closed - Opened by yashumayank almost 3 years ago

#397 - presence on Maven repository

Issue - State: closed - Opened by GuilhemSempere almost 3 years ago

#392 - Choose snpEff release to download (especially release 5.0e)

Issue - State: closed - Opened by antonylebechec almost 3 years ago - 2 comments

#387 - Extracting SNP degeneracy information

Issue - State: closed - Opened by connor122721 almost 3 years ago

#382 - Wheat reference : IWGSCv1.0

Issue - State: closed - Opened by Roopali87 almost 3 years ago

#380 - Checking matches between database reference genome

Issue - State: closed - Opened by hclendenin about 3 years ago

#378 - Need some help to build custom genome

Issue - State: closed - Opened by Abieskawa about 3 years ago - 2 comments

#377 - mm39 database download error

Issue - State: closed - Opened by akhilvelluva about 3 years ago - 1 comment

#376 - Trouble creating custom db using files from NCBI

Issue - State: closed - Opened by kyaki about 3 years ago

#375 - Missing some images in output snpEff_summary.html file.

Issue - State: closed - Opened by jhxaz about 3 years ago - 1 comment

#371 - SnpEff does not follow HGVS guidelines for multi-AA substitution events

Issue - State: closed - Opened by m-crown about 3 years ago - 2 comments

#361 - "-no-intergenic" option does not work

Issue - State: closed - Opened by uceleste about 3 years ago - 1 comment

#360 - snpsift annotate with -id flag not working

Issue - State: closed - Opened by msnyder424 about 3 years ago

#359 - error while annotatin for geneid

Issue - State: closed - Opened by ghost about 3 years ago

#358 - Annotation error of duplication at exon edge

Issue - State: closed - Opened by kimi641 over 3 years ago

#357 - Error: string index out of range

Issue - State: closed - Opened by martipujolar over 3 years ago

#356 - Issue with the Mnemiopsis leidyi database

Issue - State: closed - Opened by martipujolar over 3 years ago

#355 - Marking duplication as insertion

Issue - State: closed - Opened by yaarau over 3 years ago - 1 comment