Ecosyste.ms: Issues

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GitHub / mskcc/vcf2maf issues and pull requests

#361 - Is there any T2T chm13 genome support?

Issue - State: open - Opened by liuyang2006 1 day ago

#358 - maf2maf issue

Issue - State: open - Opened by parvathisudha 3 months ago

#357 - adding plugin parameter to vcf2maf

Pull Request - State: open - Opened by allaway 3 months ago

#356 - error with VEP

Issue - State: closed - Opened by complexgenome 3 months ago - 1 comment

#355 - docker clone

Issue - State: closed - Opened by complexgenome 3 months ago - 1 comment

#354 - traying to make a maf from an already annotated vcf

Issue - State: open - Opened by javierAPC 5 months ago

#353 - vcf2maf generates an empty maf file

Issue - State: open - Opened by Olsennnnn 6 months ago

#352 - Normalization of vcf file

Issue - State: open - Opened by celine-weng 6 months ago

#350 - Remove deprecated VEP 110 argument

Pull Request - State: closed - Opened by MatthijsPon 9 months ago

#349 - Unrecognized biotype/effect

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

#347 - Error Argument "" isn't numeric in subtraction

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

#345 - cosmic annotation

Issue - State: open - Opened by me-nobody about 1 year ago

#344 - VCF2MAF and allele frequency

Issue - State: open - Opened by jmf432x over 1 year ago - 4 comments

#343 - The best solution for one-to-one correspondence between genes and transcripts

Issue - State: open - Opened by user-tq over 1 year ago - 3 comments

#342 - ERROR: Failed to run the VEP annotator!

Issue - State: open - Opened by SuiyueWestlake over 1 year ago

#340 - Release new tag

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

#339 - Update vcf2maf to work with later Ensembl vep releases

Issue - State: open - Opened by tamuanand over 1 year ago - 2 comments

#338 - ERROR: Provided --ref-fasta is missing or empty

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

#337 - Option --retain-fmt doesn't work

Issue - State: open - Opened by YussAb over 1 year ago

#336 - Why is empty in all database?

Issue - State: open - Opened by xiasijian over 1 year ago - 1 comment

#335 - Running error

Issue - State: open - Opened by KasitC almost 2 years ago - 3 comments

#334 - ERROR: Failed to run the VEP annotator!

Issue - State: open - Opened by EsterAH almost 2 years ago - 2 comments

#333 - Add options for RefSeq and Merged caches when converting to MAF

Issue - State: open - Opened by bkohrn almost 2 years ago

#332 - Empty 't_depth' 't_ref_count' 't_alt_count'

Issue - State: open - Opened by QingruXu44004 about 2 years ago - 1 comment

#331 - handle file names and paths which contain special characters

Pull Request - State: closed - Opened by xnr13 about 2 years ago - 1 comment

#330 - Losing info when reading maf file

Issue - State: open - Opened by eibol1 about 2 years ago

#329 - --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410

Issue - State: closed - Opened by eibol1 about 2 years ago - 2 comments

#328 - Remove --af_esp for compatibility with v107 ensemble

Pull Request - State: closed - Opened by allaway about 2 years ago - 1 comment

#327 - how to run vcf2maf with clinvar db

Issue - State: open - Opened by songeric1107 about 2 years ago - 2 comments

#325 - Unknown option: af_esp ERROR: Failed to parse command-line flags

Issue - State: closed - Opened by biginfor about 2 years ago - 5 comments

#324 - Remove --af_esp flag as it's deprecated

Pull Request - State: closed - Opened by bozbezbozzel about 2 years ago - 1 comment

#322 - gnomad and esp AF deprecated in VEP v107

Issue - State: open - Opened by prmac about 2 years ago - 3 comments

#321 - Structural variant without CHR2

Issue - State: open - Opened by j-hudecek about 2 years ago

#320 - Handle new splice effects in ensembl-vep version 105

Pull Request - State: closed - Opened by GFJHogue about 2 years ago - 1 comment

#319 - --ref-fasta missing or empty

Issue - State: closed - Opened by Rozita1 over 2 years ago

#318 - vcf2maf.pl: --vep-stats to work around VEP bug

Pull Request - State: closed - Opened by alanhoyle over 2 years ago - 4 comments

#315 - Bio::EnsEMBL::Registry package

Issue - State: open - Opened by jingydz over 2 years ago

#314 - Cannot find VEP script under

Issue - State: open - Opened by jingydz over 2 years ago - 1 comment

#311 - Reference file not working

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

#310 - vcf2maf could not specify the output path

Issue - State: open - Opened by songeric1107 over 2 years ago - 1 comment

#309 - Choose Transcript when converting VCF to MAF

Issue - State: open - Opened by Wangxin555 over 2 years ago

#308 - Can't locate Bio/PrimarySeqI.pm in @INC issue

Issue - State: open - Opened by gaom001 over 2 years ago

#307 - How to keep values of Count, Coverage and Frequency in the maf file

Issue - State: open - Opened by gonzalo253 over 2 years ago - 1 comment

#306 - Could vcf2maf specify fields and then rename them?

Issue - State: open - Opened by shzyjbren almost 3 years ago

#305 - VCF2MAF failed to run

Issue - State: open - Opened by GACGAMA almost 3 years ago - 1 comment

#304 - Inhibit VEP But FASTA File Required

Issue - State: open - Opened by DarioS almost 3 years ago

#303 - Cannot find VEP script variant_effect_predictor.pl in path:

Issue - State: closed - Opened by ksingh1119 almost 3 years ago

#302 - Failed to run the VEP annotator

Issue - State: open - Opened by zyh4482 almost 3 years ago - 4 comments

#301 - Commands not supported by windows

Issue - State: open - Opened by jrcodina almost 3 years ago

#300 - Problem with "Unknown option: af_gnomad"

Issue - State: open - Opened by MjelleLab almost 3 years ago - 1 comment

#298 - Some columns of the MAF file are empty

Issue - State: open - Opened by Rui-Jing about 3 years ago - 1 comment

#297 - Preserve multisample genotype fields in the maf format

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

#296 - Can I convert the annotated VCF file to MAF?

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

#295 - How to have a vcf_region in maf file

Issue - State: open - Opened by Anahit19 about 3 years ago

#294 - how to retain INFO columns in maf2vcf?

Issue - State: open - Opened by anoronh4 about 3 years ago - 1 comment

#292 - Genome Build Compatibility Issues

Issue - State: open - Opened by Jay-Leung about 3 years ago - 5 comments

#291 - maf2vcf.pl doesn't recognise N bases

Issue - State: open - Opened by shadihames about 3 years ago - 3 comments

#290 - issue converting VEP.vcf file to maf

Issue - State: open - Opened by iichelhadi about 3 years ago - 3 comments

#289 - --vep-custom doesnt keep the FILTER flags

Issue - State: open - Opened by apinto-helomics over 3 years ago

#288 - vcf2maf deal with vcf files with multiple samples

Issue - State: open - Opened by xiw588 over 3 years ago - 1 comment

#286 - dbSNP field is not kept

Issue - State: closed - Opened by Anahit19 over 3 years ago - 5 comments

#285 - problems with allelic frequency

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

#284 - POD changed, external exec params

Pull Request - State: closed - Opened by alanhoyle over 3 years ago

#283 - Parameterized subprocesses and POD --help/--man changes.

Pull Request - State: closed - Opened by alanhoyle over 3 years ago - 3 comments

#279 - vcf2maf removal of anchor bases on complex variants

Issue - State: closed - Opened by andurill over 3 years ago - 8 comments

#278 - vcf2maf prioritises 3'UTR over missense variant

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

#274 - vcf2maf can not report VEP custom database annotation?

Issue - State: closed - Opened by tangwei1129 almost 4 years ago - 11 comments

#245 - Strange Behavior Regarding Chromosomes

Issue - State: closed - Opened by Slavatron over 4 years ago - 1 comment

#243 - vcf2maf error: Can't locate Bio/PrimarySeqI.pm in @INC

Issue - State: closed - Opened by matnguyen over 4 years ago - 5 comments

#242 - vcf2maf error

Issue - State: closed - Opened by msubirana over 4 years ago - 1 comment

#240 - missing t_depth/t_alt_count/t_ref_count fields in MAF files

Issue - State: closed - Opened by ltang217 over 4 years ago - 2 comments

#239 - Does Reference_Allele mean allele in the reference genome?

Issue - State: closed - Opened by singletrips over 4 years ago - 1 comment

#238 - Install Problems in a university cluster

Issue - State: closed - Opened by ShaowenJ over 4 years ago - 2 comments

#234 - Splitting regions to samtools still causing variant loss

Issue - State: open - Opened by pwwang almost 5 years ago

#228 - vcf2maf - HGVSc column

Issue - State: open - Opened by kcourtet about 5 years ago - 2 comments

#227 - Incorrect Entrez-Hugo Symbol mapping of chr1, 13365776

Issue - State: open - Opened by thomasyu888 over 5 years ago - 1 comment

#223 - Why does vcf2maf filter out CNV / Fusion/ ProcControl / RNAExonVariant ?

Issue - State: closed - Opened by lakhujanivijay over 5 years ago - 1 comment

#204 - ERROR: Failed to run the VEP annotator!

Issue - State: open - Opened by neilihrke almost 6 years ago - 8 comments

#184 - retain info from FORMAT field vcf2maf

Issue - State: open - Opened by anabbi about 6 years ago - 2 comments