So, I have 8 normal sample and 8 tumor sample. Each normal and tumor group had been processed to get mpileup file by samtools. After that, I did the varscan2 soomatic function to call variation. After that, I got warning resetting normal and from what I found in the document, it's better to not call mpileup for each group. Instead, calling mpileup for 2 bam file, 1 normal and 1 tumor. So, I had finished doing this. I take 1 normal sample and 1 tumor sample for mpileup input to generate 1 mpileup file. After that, I use that mpileup file for varscan input. The result is no warning and seems no problem. My question is, how do I integrate the result for 8 normal/tumor pair varscan results? I figure if I proocess the data with 1 normal and 1 tumor, I will need to do varscan call 8 times and will get 8 results. Is there any method to join the results?