VarScan2 copynumber output name

nstickle · 08-25-2015, 01:23 PM

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 · 01-30-2018, 04:43 PM

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 · 08-29-2018, 07:21 AM

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!

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08-25-2015, 01:23 PM	#1
nstickle Junior Member Location: Toronto, ON Join Date: Mar 2013 Posts: 1	VarScan2 copynumber output name 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?

01-30-2018, 04:43 PM	#2
amalthomas111 Junior Member Location: Los Angeles Join Date: Oct 2015 Posts: 1	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 Last edited by amalthomas111; 01-30-2018 at 05:39 PM.

08-29-2018, 07:21 AM	#3
kasadevall Junior Member Location: Barcelona Join Date: Aug 2018 Posts: 1	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!