Questions tagged [maf]

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merge two maf objects

I am trying to use maftools to analyze some data. I already have two maf files and I could load them into R and analyze both. For each of them, the ...
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Problems when using vcf2maf

I am trying to use a commonly recommended package named vcf2mafto convert vcf file to maf file and is reliant on Ensembl's Variant Effect Predictor (VEP) here. However, if I follow the guidelines ...
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Error in installing vcf2maf

I tried to install vcf2maf following this tutorial from GitHub: https://github.com/mskcc/vcf2maf. I get a repeat error when I try to test out vcf2maf using the code:...
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An error with annovar

I want to install annovar but in one particular part I always get this error ...
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How to chose values for QC for a GWAS?

I am running a GWAS on a large dataset. I am using the H3aBioNet QC workflow (https://github.com/h3abionet/h3agwas/blob/master/qc/README.md). I have run the QC on initial parameters: MAF < 0.01 ...
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How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
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2 answers
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Merging matched parts of two dataframes

I have a big data frame like this ...
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177 views

maf file format: Variant_Classification value for non frameshift substitution

I have a vcf containing SNV and MNV (short indells or substitutions), I have annotated that file with annovar and in the resulting txt file I have this row: ...
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How to select point mutations from MAF file

I am using a mutation MAF file from GDC. I want to select for point mutations, therefore I selected Variant_Classification equal to ...
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GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String

I have installed GMAJ using: ...
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8 votes
2 answers
5k views

Tools to do VCF to MAF and MAF to VCF conversion?

Normally, I would use the vcf2maf scripts to convert a VCF to a MAF (or vice versa). This is great software, but on my system, perl scripts with dependencies are easy to break. (Here it uses VEP.) ...
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2 votes
1 answer
747 views

Downloading an open-source MAF with tumor and normal BAMs?

I'm writing an R package that manipulates MAF files. Normally, I generate a small example of a file and use this for testing. (e.g. a subsetted BAM or MAF). In this case, I would need a MAF and a ...
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