Questions tagged [maf]
The maf tag has no usage guidance.
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 ...
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 ...
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:...
An error with annovar
I want to install annovar but in one particular part I always get this error ...
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 ...
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 ...
Merging matched parts of two dataframes
I have a big data frame like this ...
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: ...
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 ...
GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
I have installed GMAJ using: ...
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.) ...
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 ...