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  • Transform VCF file for Rqtl input for genetic mapping

    Hi everyone,

    I am trying to find out if there is any tools out there to transform a VCF file to make input file for Rqtl or similar tool.
    Basically, I have WGS for RIL population (180 lines) for which I did variant calling using samtools and have a VCF file that i need to parse it to get an input file for linkage/QTL mapping tools such as Rqtl or QTL cartographer. Please suggest if there are any tools. Any help is appreciated.

    Thank you.

    -Raj

  • #2
    Here's a python script that may be what you want:
    reference-free ddRADseq analysis tools. Contribute to brantp/rtd development by creating an account on GitHub.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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    • #3
      cross posted https://www.biostars.org/p/150009/

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