TCGA documentation for the MAFs (mutation annotation files) have
Allele2 versions of similar values; what is the difference between these alleles?
For instance, I am interested in
Tumor_Seq_Allele but not sure whether to use
Tumor_Seq_Allele2. I am looking at data for ACC (Adrenocortical carcinoma) tumors, and for many of the mutations,
Tumor_Seq_Allele1 is actually the same as the reference allele. Which one is the actual mutation?
Thank you in advance! For reference, this is the documentation I am looking at: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/