I am working on a somatic signatures project and I would like to make somatic signatures of the 80 Uveal Melanoma samples on the TCGA site but I encounter some problems.
First: how can I transform .MAF files from the TCGA site in to .VCF file in order to use the vr_A = readVcfAsVRanges(vcf_A_path, "GenomeA") command in Rstudio?
Second: how can I use and upload the reference genome in my Rstudio used for the Uveal Melanoma. I know they used the HG19 build available on this link https://browser.cghub.ucsc.edu/help/assemblies/
Third: after having this worked out I would like to follow the steps described in the somatic signature vignette eventually leading to the use of this command: plotMutationSpectrum(sca_motifs, "study")
Probably I am tackling this problem the other way around but because Uveal Melanoma is not available in the online data after entering this code from the vignette sca_metadata = scaMetadata() I have to try something else.
I am a beginner in this field and I hope you are willing to answer (some) the questions and help me out.
Thanks in advance