n_lod t_lod_fstar t_lod_fstar__INFO__ n_genotype n_ref_count n_alt_count
50.33 PASS 16.43 0/0 448 149
n_allelic_depth n_QSS n_alt_allele_seen i_n_REF_F1R2 i_n_REF_F2R1
448,149 14273 False 214 234
i_n_ALT_F1R2 i_n_ALT_F2R1 i_n_Foxog n_tumor_f t_genotype t_ref_count
0 0 NA 0.135 0/1 457
t_alt_count t_allelic_depth t_QSS t_alt_allele_seen i_t_REF_F1R2
55 457,55 15045 True 223
i_t_REF_F2R1 i_t_ALT_F1R2 i_t_ALT_F2R1 i_t_Foxog t_tumor_f
234 1 4 0.8 0.059
This is from out put from MuTect2, and I annotate it with Oncotator.
I pasted only the scores for the mutation. The names with "n" are for normal sample, the names with "t" are for tumor sample.
Strange things:
(1) How come the tumor fraction in normal sample is 0.135, even higher than that in tumor sample 0.059?
(2) n_alt_count is 149, but n_alt_allele_seen is false, and both i_n_ALT_F1R2 and i_n_ALT_F2R1 are 0.