converting VCF to MAF fro mouse data
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5.0 years ago
ksymeonidh ▴ 10

Dear all, I am currently working on tumors from mouse data and I would like to run MuSiC in order to identify significantly mutated genes. The SNP calling has been done with Strelka and as reference I used the mm9 UCSC genome. I am stuck however in the creation of the MAF files. I have tried the vcf2maf.pl script with the snpEff option, but the file created has no information, i.e. no gene symbols of type of effect etc. Do you have any idea how to create MAF files? Thank you.

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I had the same problem and it got clarified from this forum only. Actually, the reason you are not getting any gene names is due to your variants falling inside the intergenic region. You can't really get gene names for variants falling in the non-coding region of the genes.

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