Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / mskcc/vcf2maf issues and pull requests
#362 - ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build
Issue -
State: open - Opened by liuyang2006 1 day ago
#361 - Is there any T2T chm13 genome support?
Issue -
State: open - Opened by liuyang2006 1 day ago
#360 - ERROR: No cache found for homo_sapiens, version 93
Issue -
State: open - Opened by Olsennnnn 18 days ago
#359 - Running vcf2maf WARNING: No genotype column for NORMAL in VCF! WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
Issue -
State: open - Opened by tanayb001 about 2 months 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
#351 - Empty 't_depth' 't_ref_count' 't_alt_count' from VCF with format GT:GL:GOF:GQ:NR:NV
Issue -
State: open - Opened by ChristianRohde 8 months ago
- 1 comment
#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
#348 - WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority!
Issue -
State: closed - Opened by ilovegreentea about 1 year ago
- 1 comment
#347 - Error Argument "" isn't numeric in subtraction
Issue -
State: closed - Opened by complexgenome about 1 year ago
- 2 comments
#346 - HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108
Issue -
State: open - Opened by ChristianRohde about 1 year ago
- 3 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
#341 - ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID
Issue -
State: open - Opened by gjoseph15 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
#326 - ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.
Issue -
State: open - Opened by melodyeeeee about 2 years ago
- 3 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
#323 - I have a annotationed vep.vcf file, can I use vcf2maf to convert MAF without installing VEP?
Issue -
State: closed - Opened by aaaniich 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
#317 - n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation
Issue -
State: open - Opened by sggaffney over 2 years ago
#316 - (1.6.21) Not able to use all available CPU threads in the later part of VEP
Issue -
State: open - Opened by sclan over 2 years ago
#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
#313 - Attempt to reload Bio/EnsEMBL/IO/Parser.pm aborted. Compilation failed in require at /usr/share/perl5/vendor_perl/parent.pm line 20.
Issue -
State: closed - Opened by cancer-oncogenomics over 2 years ago
#312 - Is c_pos suppose to match negative numbers in vcf2maf.pl ?
Issue -
State: open - Opened by kimin0402 over 2 years ago
#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
#299 - I have a annotationed vep.vcf file, can I use vcf2maf to convert MAF without installing VEP?
Issue -
State: open - Opened by xuexidaima 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
#293 - Feature Request: Add options to allow for use of refseq or merged caches from VEP
Issue -
State: open - Opened by bkohrn about 3 years ago
#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
#287 - --max-subpop-af: how can this option be deactivated and can it be applied to other populations?
Issue -
State: open - Opened by ISmolicz over 3 years ago
- 3 comments
#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
#257 - ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 390.
Issue -
State: closed - Opened by HaileyHryPark about 4 years ago
- 12 comments
#250 - Can't exec "/bin/sh": Argument list too long at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376.
Issue -
State: closed - Opened by anishchakka over 4 years ago
- 1 comment
#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
#241 - Failed to synchronize cache for repo 'AppStream', ignoring this repo. The command '/bin/sh -c yum install wget java-1.8.0-openjdk-devel -y' returned a non-zero code: 1
Issue -
State: closed - Opened by paramacharya 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
#229 - ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf
Issue -
State: closed - Opened by milgri about 5 years ago
- 6 comments
#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
#222 - Error encountered while running vcf2maf: Bio::PrimarySeqI module is missing
Issue -
State: closed - Opened by lakhujanivijay over 5 years ago
- 3 comments
#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