Some paper use D-ToxoG to filter oxog artifacts after running** Mutect1** (not Mutect2) .
But D-ToxoG input needs some specific columns that common MAF or VCF file didn't provide.
For example,
i_t_ALT_F1R2，i_t_ALT_F2R1，i_t_REF_F1R2，i_t_REF_F2R1，i_t_Foxog。
(In addition, Is "ref_context" only provided by oncotator ?)。
So i wonder how to get these information after running Mutect1 (or other tool except Mutect2)
Thanks !