VarScan2 copynumber output name

[nstickle]

Hi. I have been running VarScan2 copynumber
according to the manual's instructions, shown here:

samtools mpileup -q 1 -f ref.fa normal.bam tumor.bam |
java -jar VarScan.jar copynumber varScan --mpileup 1
This will create a single output file, varScan.copynumber, containing the raw copynumber calls.

My exact command is:

samtools mpileup -B -q 10 -f genome.fa normal.bam tumor.bam |\
awk -F"\t" '$4 > 0 && $7 >0' | java -jar $varscan_dir/VarScan.jar copynumber \
tumor.copynumber --mpileup 1 --data-ratio 0.50

The problem is that it is not writing the output to my file "tumor.copynumber" but instead to "output.copynumber" which is the default. Anyone have any idea why?

[amalthomas111]

Facing same issue

Did you figure out a solution for this?

I tried this:

varscan=~/VarScan.v2.3.9.jar

samtools mpileup -q 1 -B -f ${ref_fasta} ${normalbam} ${tumorbam} |java -jar ${varscan} copynumber --mpileup ${outputname} 1

This seems working, though in VarScan2 copynumber page it is mentioned:

samtools mpileup -q 1 -f ref.fa normal.bam tumor.bam |
java -jar VarScan.jar copynumber <outputname> --mpileup 1

Which is not working!

Using:

$ samtools --version
samtools 1.5
Using htslib 1.5
Copyright (C) 2017 Genome Research Ltd.

$
VarScan v2.3

[kasadevall]

Order matters apparently

I had the same problem and apparently solved by putting the name of the output file just after the combined pileup file and before the "--mpileup 1" argument

java -jar VarScan.v2.3.9.jar copynumber tumor_normal.mpileup OUTPUTNAME --mpileup 1 --min-coverage 10 (etc etc if you want to add other options)

The output of this command should be OUTPUTNAME.copynumber (the .copynumber is always added by Varscan).

Hope it helps!