can VarScan2 do joint somatic calling?

Question

[Zoey Zou]

Hi,

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.

Regards,

Zoey

Answer 1

[ATpoint]

Does it mean that I can only do somatic calling for one pair of normal-tumor sequence each time

Yes, from what I understand VarScan2 is not designed for joint calling.

[Zoey Zou]

Hi, Appreciate for your help. I just realized that I did not have a good understanding of somatic calling. And I found that in the GATK website it explained that "there is currently no way to perform joint calling for somatic variant discovery". Maybe I can find another method to put the snvs together to build the tree.