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  • Aristotle
    Junior Member
    • Apr 2018
    • 1
    #1

    Variant calling using CRISP

    hELLO,
    I'm new to bioinformatics, and to the SEQ answers forum as well.
    I am trying to analyze NGS data for 8 pools of 12 samples each. I am currently stuck at variant calling as CRISP seems to not detect any variants.
    I have altered the minimum base quality (I have used mbq of 10 to 30) and minimum mapping quality. I suspect the problem may be from my reference sequence as I get this output which says
    "reading chromosome chr13 offset 412481050"... and I suspect this isnot right because I am working with the APOE locus which is on chromosome 19.

    Please how may I resolve this?
    Tags: crisp, ngs analysis, variant calling
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