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

Thanks!Wei