When re-oncotating an input TCGAMAF, alias fields in the defaults file (source=WXS,status=Somatic,phase=Phase_I,sequencer=Illumina GAIIx) overwrite the associated fields for every mutation in the output TCGAMAF, putting the original values in i_* fields, rather than only being used when the fields are unpopulated.
When re-oncotating an input TCGAMAF, alias fields in the defaults file (
source=WXS,status=Somatic,phase=Phase_I,sequencer=Illumina GAIIx) overwrite the associated fields for every mutation in the output TCGAMAF, putting the original values ini_*fields, rather than only being used when the fields are unpopulated.Example Input MAF: TCGA-AA-3877-01.hg19.maf.txt
Example Output MAF: TCGA-AA-3877-01.hg19.oncotator.maf.txt