I've heard that we can't infer heterozygosity or homozygosity for the mutations identified in MAF files, but I noticed that the MAF file's columns 11-13 may have information for inferring this info. For example
Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
G G C
G G C
A A C
G G A
C C T
C C A
From a comparison of Ref and Tumor alleles, can we infer that all these mutations are heterozygous? because One tumor allele is the same as Ref allele. Is this understanding correct?
I am still veray confused .so what's the actual meaning of Tumor-Seq-Allele1 and Tumor-Seq-Aelle2
The two alleles observed in the tumor sequencing data which MAF format assumes is diploid.