How to apply GenVisR Bioconductor package on VCF file

Question

[kay]

Hello,

I have a VCF file and I am looking to apply the GenVisR Bioconductor package, so I can create a waterfall plot.

I read the documentation and was not sure if it will accept VCF file format, or whether I need to convert the VCF into MAF or MGI .

Any pointers on how to get this package working on VCF file will be helpful

Thanks, K

Answer 1

[theobroma22]

The input to waterfall consists of a data frame derived from either a .maf (version 2.4) file or a file in MGI annotation format (obtained from The Genome Modeling System) specified via the fileType parameter.

https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/GenVisR_intro.html

Answer 2

[zlskidmore]

Unfortunately GenVisR cannot accept VCF files at this time, for now the best approach will be to set the fileType param to "custom", you will then be able to provide a data frame with the required columns "sample", "gene", "variant_class". You will also need to fill in the parameter "variant_class_order" which takes a character vector specifying the order preference for each variant class. For example if you had both a missense and nonsense mutation for the same gene/sample the one plotted would depend on the "variant_class_order" param.

There is a vignette specific to the waterfall function here as well that you might find usefull.

https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/waterfall_introduction.html

Zach

Answer 3

[kay]

Thank you for all this feedback.

I did manage to convert my VCF to MAF file. But am unable to read the MAF file into my R since I have an older R version due to my Mavericks OS.

So I'm trying to do a workaround with this "custom" file type. Is there an easy way to convert the MAF file format into this custom file format. I'm not very familiar with MAF file formats, so would appreciate any advise on this . Thanks !

[zlskidmore]

you should be able to read in your maf file right into R with read.delim() (if your maf also has the secondary header giving the maf version remove that). From there you should be able to just rename the appropriate columns of the data frame to conform with the "custom" fileType

[ahorn720]

Hey Krithika.gu, How did you convert the VCF to MAF? I've been trying to do it with vcf2maf.pl without much luck but maybe you have a better way to do it. I to have been trying to use GeneVisR.

Thank you!

[kay]

Hey, I tried to use all these packages, I was able to convert VCF to MAF using https://github.com/mskcc/vcf2maf, but they did not give me the right answer. From my understanding, these packages work well only if you have a smaller filtered VCF file of somatic mutations. If you use the original VCF, these packages will not work well.