I am trying to use different mutation analysis pipelines(muse, mutect for my tumor samples using TCGABiolinks package. I want to use hg19 as the reference genome.
However it seems that I can only specify the certain pipeline using "pipeline="muse" in "GDCquery_maf()" which is used when our reference is hg38.
For hg19, GDCquery() function is used, but it is not clear which pipeline is used and how we can specify our desired pipeline.
I am looking forward to your comments