Issues
- 0
maf2maf issue
#358 opened by parvathisudha - 3
gnomad and esp AF deprecated in VEP v107
#322 opened by prmac - 1
docker clone
#355 opened by complexgenome - 1
error with VEP
#356 opened by complexgenome - 3
- 4
Release new tag
#340 opened by pdiakumis - 1
WARNING: Unrecognized effect "sequence_feature". Assigning lowest priority!
#348 opened by ilovegreentea - 0
traying to make a maf from an already annotated vcf
#354 opened by javierAPC - 0
vcf2maf generates an empty maf file
#353 opened by Olsennnnn - 0
Normalization of vcf file
#352 opened by celine-weng - 5
- 1
Empty 't_depth' 't_ref_count' 't_alt_count' from VCF with format GT:GL:GOF:GQ:NR:NV
#351 opened by ChristianRohde - 4
VCF2MAF and allele frequency
#344 opened by jmf432x - 2
Unrecognized biotype/effect
#349 opened by hosseinvk - 2
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf.
#326 opened by melodyeeeee - 3
HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108
#346 opened by ChristianRohde - 3
ERROR: Provided --ref-fasta is missing or empty
#338 opened by medbenamine - 4
Failed to run the VEP annotator
#302 opened by zyh4482 - 2
Error Argument "" isn't numeric in subtraction
#347 opened by complexgenome - 2
- 0
cosmic annotation
#345 opened by me-nobody - 2
ERROR: Failed to run the VEP annotator!
#334 opened by EsterAH - 0
ERROR: Failed to run the VEP annotator!
#342 opened by SuiyueWestlake - 0
- 0
Option --retain-fmt doesn't work
#337 opened by YussAb - 1
vcf2maf could not specify the output path
#310 opened by songeric1107 - 1
Why is empty in all database?
#336 opened by xiasijian - 3
Running error
#335 opened by KasitC - 1
- 0
- 2
--ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410
#329 opened by eibol1 - 1
Empty 't_depth' 't_ref_count' 't_alt_count'
#332 opened by QingruXu44004 - 0
Losing info when reading maf file
#330 opened by eibol1 - 2
how to run vcf2maf with clinvar db
#327 opened by songeric1107 - 1
I have a annotationed vep.vcf file, can I use vcf2maf to convert MAF without installing VEP?
#323 opened by aaaniich - 1
VCF2MAF failed to run
#305 opened by GACGAMA - 0
Structural variant without CHR2
#321 opened by j-hudecek - 0
--ref-fasta missing or empty
#319 opened by Rozita1 - 0
n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation
#317 opened by sggaffney - 1
Cannot find VEP script under
#314 opened by jingydz - 0
- 0
Bio::EnsEMBL::Registry package
#315 opened by jingydz - 0
Attempt to reload Bio/EnsEMBL/IO/Parser.pm aborted. Compilation failed in require at /usr/share/perl5/vendor_perl/parent.pm line 20.
#313 opened by cancer-oncogenomics - 0
- 1
Reference file not working
#311 opened by camcecc - 0
Choose Transcript when converting VCF to MAF
#309 opened by Wangxin555 - 0
Can't locate Bio/PrimarySeqI.pm in @INC issue
#308 opened by gaom001 - 0
Could vcf2maf specify fields and then rename them?
#306 opened by shzyjbren - 0
Inhibit VEP But FASTA File Required
#304 opened by DarioS - 0