mskcc vcf2maf issues - Githubissues

mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

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ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build

#362 liuyang2006 opened 2 days ago
0
Is there any T2T chm13 genome support?

#361 liuyang2006 opened 2 days ago
0
ERROR: No cache found for homo_sapiens, version 93

#360 Olsennnnn opened 2 weeks ago
0
Running vcf2maf WARNING: No genotype column for NORMAL in VCF! WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!

#359 tanayb001 opened 2 months ago
0
maf2maf issue

#358 parvathisudha opened 2 months ago
0
adding plugin parameter to vcf2maf

#357 allaway opened 2 months ago
0
error with VEP

#356 complexgenome closed 3 months ago
1
docker clone

#355 complexgenome closed 3 months ago
1
traying to make a maf from an already annotated vcf

#354 javierAPC opened 5 months ago
0
vcf2maf generates an empty maf file

#353 Olsennnnn opened 5 months ago
0
Normalization of vcf file

#352 celine-weng opened 6 months ago
0
Empty 't_depth' 't_ref_count' 't_alt_count' from VCF with format GT:GL:GOF:GQ:NR:NV

#351 ChristianRohde opened 7 months ago
1
Remove deprecated VEP 110 argument

#350 MatthijsPon closed 4 months ago
0
Unrecognized biotype/effect

#349 hosseinvk opened 1 year ago
2
WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority!

#348 ilovegreentea closed 4 months ago
1
Error Argument "" isn't numeric in subtraction

#347 complexgenome closed 1 year ago
2
HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108

#346 ChristianRohde opened 1 year ago
3
cosmic annotation

#345 me-nobody opened 1 year ago
0
VCF2MAF and allele frequency

#344 jmf432x opened 1 year ago
4
The best solution for one-to-one correspondence between genes and transcripts

#343 user-tq opened 1 year ago
3
ERROR: Failed to run the VEP annotator!

#342 SuiyueWestlake opened 1 year ago
0
ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID

#341 gjoseph15 opened 1 year ago
0
Release new tag

#340 pdiakumis closed 4 months ago
4
Update vcf2maf to work with later Ensembl vep releases

#339 tamuanand opened 1 year ago
2
ERROR: Provided --ref-fasta is missing or empty

#338 medbenamine closed 1 year ago
3
Option --retain-fmt doesn't work

#337 YussAb opened 1 year ago
0
Why is empty in all database?

#336 xiasijian opened 1 year ago
1
Running error

#335 KasitC opened 1 year ago
3
ERROR: Failed to run the VEP annotator!

#334 EsterAH opened 1 year ago
2
Add options for RefSeq and Merged caches when converting to MAF

#333 bkohrn opened 1 year ago
0
Empty 't_depth' 't_ref_count' 't_alt_count'

#332 QingruXu44004 opened 2 years ago
1
handle file names and paths which contain special characters

#331 xnr13 closed 1 year ago
1
Losing info when reading maf file

#330 eibol1 opened 2 years ago
0
--ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410

#329 eibol1 closed 2 years ago
2
Remove --af_esp for compatibility with v107 ensemble

#328 allaway closed 2 years ago
1
how to run vcf2maf with clinvar db

#327 songeric1107 opened 2 years ago
2
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.

#326 melodyeeeee opened 2 years ago
3
Unknown option: af_esp ERROR: Failed to parse command-line flags

#325 biginfor closed 2 years ago
5
Remove --af_esp flag as it's deprecated

#324 bozbezbozzel closed 4 months ago
1
I have a annotationed vep.vcf file, can I use vcf2maf to convert MAF without installing VEP?

#323 aaaniich closed 2 years ago
1
gnomad and esp AF deprecated in VEP v107

#322 prmac opened 2 years ago
3
Structural variant without CHR2

#321 j-hudecek opened 2 years ago
0
Handle new splice effects in ensembl-vep version 105

#320 GFJHogue closed 1 year ago
1
--ref-fasta missing or empty

#319 Rozita1 closed 2 years ago
0
vcf2maf.pl: --vep-stats to work around VEP bug

#318 alanhoyle closed 2 years ago
4
n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation

#317 sggaffney opened 2 years ago
0
(1.6.21) Not able to use all available CPU threads in the later part of VEP

#316 sclan opened 2 years ago
0
Bio::EnsEMBL::Registry package

#315 jingydz opened 2 years ago
0
Cannot find VEP script under

#314 jingydz opened 2 years ago
1
Attempt to reload Bio/EnsEMBL/IO/Parser.pm aborted. Compilation failed in require at /usr/share/perl5/vendor_perl/parent.pm line 20.

#313 cancer-oncogenomics closed 2 years ago
0