In my project, I am going to use the SNVs of different tumor regions to build the phylogenetic tree for that tumor. I am doing joint calling in different software separately. Now, I want to try VarScan2. I have one normal bam file and 10 tumor bam files from that patient. But I find that the import format for VarScan2 is:
samtools mpileup -f reference -q 1 -B normal.bam tumor.bam >normal-tumor.mpileup java -jar VarScan.jar somatic normal-tumor.mpileup normal-tumor.varScan.output --mpileup 1
Does it mean that I can only do somatic calling for one pair of normal-tumor sequence each time? How can I get the joint calling result for that?
I would appreciate any help.