Hi everyone!
I got some VCF files from different patient samples and I wanted to report most frequent mutated genes in the cohort, do survival analysis and so on (even if it is just to comprise every patient that has mutations on some gene). It is cancer samples, so it is tricky to do the analysis manually.
I had someone do most of the necessary filtering, but I am stuck on the rest.
Previously I used maftools in R ( https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html ) - but i am currently unable to do the conversion from vcf to maf. Any suggestions on tools that I can use for visualization and the sort of analysis I wanted to do?
Thanks in advance!
You may want to extract the data in the simplified form first. This tool may help
https://github.com/everestial/VCF-Simplify
You can then load the data on R or python to run the methods and statistics that fits the assumption of your data and kind of research you are doing.
I have realized that doing summary statistics and visualization of the VCF data is easier once the data is simplified.
Try following links:
1.
https://github.com/mskcc/vcf2maf
2. https://bioinformatics.stackexchange.com/questions/3421/tools-to-do-vcf-to-maf-and-maf-to-vcf-conversion
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