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Error Occurs When Running vcf2maf.pl with VCF Files Larger Than 5 MB

Status: Open.

#377 In mskcc/vcf2maf;

· km-2021 opened on Dec 10, 2025

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

vep command fails if the vcf filename has single quote

Status: Open.

#375 In mskcc/vcf2maf;

· mavwolverine opened on Sep 18, 2025

compare vep result and vcf2maf result

Status: Open.

#374 In mskcc/vcf2maf;

· Frank1219 opened on Sep 16, 2025

WARNING: No genotype column for TUMOR in VCF!

Status: Open.

#369 In mskcc/vcf2maf;

· kainamill opened on May 6, 2025

Any possibility to add <code>--retain-all-info</code>, <code>--retain-all-fmt</code> and <code>--retain-all-ann</code> arguments?

Status: Open.

#365 In mskcc/vcf2maf;

· zhuxr11 opened on Oct 25, 2024

use own fasta and gff files to annotate VCF file

Status: Open.

#364 In mskcc/vcf2maf;

· DayTimeMouse opened on Oct 15, 2024

ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build

Status: Open.

#362 In mskcc/vcf2maf;

· liuyang2006 opened on Sep 28, 2024

Is there any T2T chm13 genome support?

Status: Open.

#361 In mskcc/vcf2maf;

· liuyang2006 opened on Sep 28, 2024

ERROR: No cache found for homo_sapiens, version 93

Status: Open.

#360 In mskcc/vcf2maf;

· Olsennnnn opened on Sep 12, 2024

Running vcf2maf WARNING: No genotype column for NORMAL in VCF! WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!

Status: Open.

#359 In mskcc/vcf2maf;

· tanayb001 opened on Aug 1, 2024

maf2maf issue

Status: Open.

#358 In mskcc/vcf2maf;

· parvathisudha opened on Jul 11, 2024