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  • #1

    Where is the denovogear output?

    Dear all,
    I am trying to use DeNovoGear for DNM in trios and have used mpileup using the following command
    samtools mpileup -gDf hg19.fasta A1096.bam A1097.bam A1098.bam > trio1.bcf
    This gave me a "Segmentation fault: 11", but I decided to move on with DeNovoGear using
    "denovogear dnm auto --ped trio1.ped --bcf trio1.bcf"
    The program finished after 10 min with "Done!", but I don't see any output or error message?
    I am using Mac OS 10.7.5 with DeNovoGear 0.5.1-3-gde06767.

    Could anyone tell me whether this is a samtools issue or denovogear issue
    Best wishes,
    Ingo
    Tags: denovogear, samtools, samtools mpileup
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