I am working with RNA-seq data from TCGA and wanted to find SNVs for the datasets. The data comes in a variety of formats (VCF, MAF, and Birdseed). I've converted VCF to MAF before, but I've never worked with Birdseed. From the documentation, it seems like Birdseed files also take into account CNVs, but are there any other differences? I'd ideally like to get all of the SNVs into one file format. Can you convert Birdseed into MAF by overlapping the SNP-id with the annotation file? Are there any additional considerations I should make before converting, or are there any scripts already written for the conversion?
Thanks in advanced!