I am familiar with vcf files and clearly understand what information they provide. But for the topic I am interested in I could find only maf files. At first I thought that this is basically the same as vcf, but something did not end up. From this documentation I understood that maf files are created from multiple vcf files, but it's not clear how they are created and why in files I downloaded Reference_Allele columns are always equal to Tumor_Seq_Allele1 and Allele equal to Tumor_Seq_Allele2?
Сan I download multiple maf files from here and use Tumor_Seq_Allele_1 and Tumor_Seq_Allele_2 as cancer alleles from different patients? The task is to find most popular cancer variants from some precomputed set of positions.
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