what is the ”indel pileup file“ needed for somaticsniper fpfilter

Question

[heartheone]

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

Answer 1

[ernfrid]

You should use the tumor BAM and run samtools pileup as so:

samtools pileup -cvi -f $reference $tumor_bam > $indel_pileup_file