The manual says " Before proceeding you will need to obtain and compile bam-readcount (https://github.com/genome/bam-readcount). You will also need to generate a samtools pileup (not mpileup) indel ﬁle."
I wonder how could I get a indel pileup file?
just simply use samtools to convert normal/tumor bam?
samtools pileup -f $reference $normal_bam