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89 Open 231 Closed
89 Open 231 Closed
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Issues list

Any possibility to add --retain-all-info, --retain-all-fmt and --retain-all-ann arguments?
#365 opened Oct 25, 2024 by zhuxr11
use own fasta and gff files to annotate VCF file
#364 opened Oct 15, 2024 by DayTimeMouse
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build
#362 opened Sep 28, 2024 by liuyang2006
2
Is there any T2T chm13 genome support?
#361 opened Sep 28, 2024 by liuyang2006
ERROR: No cache found for homo_sapiens, version 93
#360 opened Sep 12, 2024 by Olsennnnn
Running vcf2maf WARNING: No genotype column for NORMAL in VCF! WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
#359 opened Aug 1, 2024 by tanayb001
maf2maf issue
#358 opened Jul 11, 2024 by parvathisudha
traying to make a maf from an already annotated vcf
#354 opened Apr 18, 2024 by javierAPC
vcf2maf generates an empty maf file
#353 opened Apr 13, 2024 by Olsennnnn
1
Normalization of vcf file
#352 opened Apr 1, 2024 by celine-weng
Empty 't_depth' 't_ref_count' 't_alt_count' from VCF with format GT:GL:GOF:GQ:NR:NV
#351 opened Feb 12, 2024 by ChristianRohde
1
Unrecognized biotype/effect
#349 opened Sep 22, 2023 by hosseinvk
2
HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108
#346 opened Jul 9, 2023 by ChristianRohde
3
cosmic annotation
#345 opened Jul 4, 2023 by me-nobody
VCF2MAF and allele frequency
#344 opened May 12, 2023 by jmf432x
4
The best solution for one-to-one correspondence between genes and transcripts
#343 opened Apr 24, 2023 by user-tq
3
ERROR: Failed to run the VEP annotator!
#342 opened Mar 24, 2023 by SuiyueWestlake
1
ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID
#341 opened Mar 21, 2023 by gjoseph15
Update vcf2maf to work with later Ensembl vep releases
#339 opened Mar 1, 2023 by tamuanand
2
Option --retain-fmt doesn't work
#337 opened Feb 9, 2023 by YussAb
Why is empty in all database?
#336 opened Jan 12, 2023 by xiasijian
1
ERROR: Failed to run the VEP annotator!
#334 opened Oct 17, 2022 by EsterAH
2
Add options for RefSeq and Merged caches when converting to MAF
#333 opened Oct 12, 2022 by bkohrn
Empty 't_depth' 't_ref_count' 't_alt_count'
#332 opened Sep 9, 2022 by QingruXu44004
1
Losing info when reading maf file
#330 opened Sep 6, 2022 by eibol1
ProTip! no:milestone will show everything without a milestone.