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  • Corrupt mpileup file?

    Hi,

    I am attempting to run a multisample mpileup.gz file (with BWA BAMs) through VarScan.

    However I get an unexpected crash that makes me think that something is dodgy with the mpileup output (See below). It looks to me like some headers are corrupt/can not be de-compressed. Many headers parse but the program drops out when after it meets malformed headers.

    Any thoughts on possible sources of this error and remedy would be appreciated.


    "LER_WGS_1_CONTIG_43240LER_WGS_1_CONTI��W��BC��G_43241LER_WGS_1_CONTIG_43242.......CONTIG_43284LER_WGS_1_CONTIG_43285LER_��"

  • #2
    Hi, could you post the exact command that you are trying to run ? Are you calling SNP's using the mpileup2snp command ?

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    • #3
      Thanks for the reply.

      The command I am attempting to exececute is

      java -jar VarScan.v2.3.2.jar mpileup2snp AllPOP.ALignment.mpileup --min-coverage 20 --min-var-freq 0.8 --p-value 0.05 -output-vcf 1

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      • #4
        Hello,

        Could you also provide the command you used to build the mpileup file, and the results of this command: "file AllPOP.ALignment.mpileup" ? It almost looks like you're feeding VarScan a compressed mpileup file.

        The input should be a raw mpileup file generated with the command "samtools mpileup -f reference -q 1 bamFile.bam".

        Comment

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