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6.7 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?
If your input is MuTect VCFs, you should be using
maf2maf. Correct? Or is there some step you didn't mention?
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.