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  • IgorFobia
    Junior Member
    • Jan 2010
    • 6

    #1

    VarScan readcounts command gives error with mpileup

    I am trying to run VarScan with readcounts option, but I keep getting this error

    Reading input from /users/fg253/new_data_drug_resistance/Co89-2/remapping_to_reference/out.sorted.rmdup.bam.mpileup
    Error: Invalid format for pileup at line null
    EK12AG100 1438119 T 0
    This is the command I'm using:
    java -jar $SW_DIR/VarScan.v2.3.6.jar readcounts $MPILEUP --min-base-qual 20 --output-file $READCOUNTS_VCF
    Can you please help me?
    Thanks

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