Can't use VarScan2 to call somatic variants from my tumor/sample vcf pair

Question

[Samuel]

Hi,

I want to call somatic variants out of my tumor vcf, using VarScan2 and the command :

java -jar VarScan.v2.3.9.jar blood.mpileup tumor.mpileup -min-coverage 10 -min-var-freq 0.08 -somatic-p-value 0.05 > test_varscan.vcf

Unfortunately, it doesn't work :

(/CONDAS/users/sbesseau/lotus) java -jar VarScan.v2.3.9.jar somatic blood.mpileup tumor.mpileup -min-coverage 10 -min-var-freq 0.08 -somatic-p-value 0.05 > test_varscan.vcf
Normal Pileup: blood.mpileup
Tumor Pileup: tumor.mpileup
Min coverage:   10x for Normal, 10x for Tumor
Min reads2:     2
Min strands2:   1
Min var freq:   0.08
Min freq for hom:       0.75
Normal purity:  1.0
Tumor purity:   1.0
Min avg qual:   15
P-value thresh: 0.99
Somatic p-value:        0.05
File Parsing Exception:  (No such file or directory)
java.io.FileNotFoundException:  (No such file or directory)
        at java.base/java.io.FileOutputStream.open0(Native Method)
        at java.base/java.io.FileOutputStream.open(FileOutputStream.java:289)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:230)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:118)
        at net.sf.varscan.Somatic.<init>(Somatic.java:931)
        at net.sf.varscan.VarScan.somatic(VarScan.java:298)
        at net.sf.varscan.VarScan.main(VarScan.java:199)
(/CONDAS/users/sbesseau/lotus) ls *mpileup
blood.mpileup  tumor.mpileup

even if I actually have all the files required in the folder ... I tried with different versions of Java but it returned the same error.

Can you help me out? Thank you very much,

Samuel

Answer 1

[Pierre Lindenbaum]

https://varscan.sourceforge.net/using-varscan.html

output is missing

usage is

USAGE: java -jar VarScan.jar somatic [normal_pileup] [tumor_pileup] [output] OPTIONS
        normal_pileup - The SAMtools pileup file for Normal
        tumor_pileup - The SAMtools pileup file for Tumor
        output - Output base name for SNP and indel output

[Samuel]

Okay it seems to work thank you.

Is this the correct output I should get?

If yes, I didn't find but is there a way to know which variants are qualified as "somatic" by varscan?

Thank you very much

[Pierre Lindenbaum]

no idea. I never used that tool.

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below)