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  • 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?

  • #2
    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, 05:39 PM.

    Comment


    • #3
      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!

      Comment

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