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vcf2maf failing to populated CAADD, REVEL, MutationTaster, Polyphenscores

Status: Open.

#381 In mskcc/vcf2maf;

· JacobAyembilla opened on Jun 20, 2026

It looks like vcf2maf cannot work with Manta (MantaBND )variants and the error given is confusing

Status: Open.

#376 In mskcc/vcf2maf;

· Manuel-DominguezCBG opened on Nov 20, 2025

ensg_to_entrez_id_map_ensembl_feb2014.tsv erroneously assigns Entrez ID

Status: Open.

#341 In mskcc/vcf2maf;

· gjoseph15 opened on Mar 21, 2023

Structural variant without CHR2

Status: Open.

#321 In mskcc/vcf2maf;

· j-hudecek opened on Jul 15, 2022

n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation

Status: Open.

#317 In mskcc/vcf2maf;

· sggaffney opened on Jun 2, 2022

Incorrect Entrez-Hugo Symbol mapping of chr1, 13365776

Status: Open.

#227 In mskcc/vcf2maf;

· thomasyu888 opened on Jun 18, 2019

maf2vcf.pl: multiple FILTER tags should be semicolon separated

Status: Open.

#209 In mskcc/vcf2maf;

· soccin opened on Dec 30, 2018

New VEP does not handle Delly SV VCFs

Status: Open.

#208 In mskcc/vcf2maf;

· ckandoth opened on Dec 26, 2018

FILTER tags of same variant from different samples are being merged

bug

Status: Open.

#142 In mskcc/vcf2maf;

· ckandoth opened on Sep 28, 2017