required data files and dependences to run maf2maf and maf2vcf
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6.8 years ago
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I have been attempting to use maf2maf to filter maf's generated from mutect output vcf's. I was under the impression that other than the input maf file, the only necessary reference file is the human genome fasta, i.e.

perl maf2maf.pl --input-maf oldmaf.maf --output-mas newmaf.maf --ref-fasta ~/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa


However, when I attempt to execute this, I get the following errors:

Use of uninitialized value $_ in substitution (s///) at ./maf2vcf.pl line 125, <GEN0> line 2786. Use of uninitialized value$_ in substitution (s///) at ./maf2vcf.pl line 125, <GEN0> line 2786. Use of uninitialized value \$al2 in string eq at ./maf2vcf.pl line 145, <GEN0> line 2786. ERROR: MAF like 2785 has no variant allele specified at 12:52282391! ERROR: Failed to run maf2vcf!


I looked at the documentation for maf2maf (and maf2vcf, which is what actually fails), and I see other input arguments --vep-path, vep-data. Are these necessary to run maf2vcf, or can it be run without installing vep?

maf2vcf maf2maf vcf2maf • 2.2k views
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If your input is MuTect VCFs, you should be using vcf2maf, not maf2maf. Correct? Or is there some step you didn't mention?

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The input is a maf file (derived from mutect vcf using someone else's script).

In any case, the problems that I'm experiencing seem to be due to a failure to obtain/install the reference data for VEP.