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vcf2maf not generating `t_depth t_ref_count t_alt_count` columns in MAF file
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17 months ago
Cancer Research UK Cambridge Institute,…

I am using vcf2maf to convert VCF files into MAF files, however the columns t_depth t_ref_count t_alt_count are empty for some new VCF files I just got, but for previous ones I do get those columns filled. I haven't managed to figure out why the new VCFs are not giving me the t_depth t_ref_count t_alt_count columns when converted to MAF, and I was hoping someone here could perhaps give me some suggestions.

The VCF that do give me those columns is version 4.1 while the one that does not give those columns is version 4.2, but in principle I think that should not matter.

I used the same code to generate the MAF file, just change names:

This produced columns:

perl $VCF2MAF --input-vcf $INPUT_VCF --output-maf $OUTPUT_MAF --tumor-id 1 --normal-id normal_kidney --vcf-tumor-id 1 --ref-fasta ~/.vep/mus_musculus/86_GRCm38/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz --filter-vcf ~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz --species mus_musculus --ncbi-build GRCm38

This didn't:

perl $VCF2MAF --input-vcf $INPUT_VCF --output-maf $OUTPUT_MAF --tumor-id B2905_Parental --normal-id SpleenKidney --vcf-tumor-id B2905.Parental.sort.bam --ref-fasta ~/.vep/mus_musculus/86_GRCm38/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz --filter-vcf ~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz --species mus_musculus --ncbi-build GRCm38

Thanks in advance for any help!

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