Questions tagged [maf]
The maf tag has no usage guidance.
12
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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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431
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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 ...
- 135
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249
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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:...
- 135
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45
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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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- 1,765
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25
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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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226
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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 ...
- 111
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2
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72
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216
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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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- 323
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53
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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 ...
- 1,773
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288
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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:
...
- 2,439
8
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2
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5k
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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.)
...
- 1,651
2
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1
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761
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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 ...
- 1,651