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  • visse226
    Junior Member
    • Nov 2016
    • 9
    #1

    Error in plink: --homozyg-window-kb flag provisionally retired

    Hi all,

    I am really new to bioinformatics and tools such as PLINK.

    I am running commands on plink data created from whole genome information. I use PLINK to search for runs of homozygosity.

    Running the default option (plink --bfile <nameoffile> --homozyg) works, but as soon as I want to change default settings, for example:
    plink --bfile <nameoffile> --homozyg-window-kb 1000 it gives me this error:
    "Error: --homozyg-window-kb flag povisionally retired, since it had no effect in PLINK 1.07"

    I do not understand this error, since I am using PLINK 1.9 (I used module load and it is also the version that comes up when i use the which command).

    Can anyone help me with this? I really need to specify my own parameter settings.

    Many thanks!
    Tags: error, plink, runs of homozygosity
  • visse226
    Junior Member
    • Nov 2016
    • 9
    #2
    By the way: I know that in plink 1.07 I will have to change the flag into --homozyg-window-snp 1000
    (I hope this is correct indeed), but I want to know what I can do if I want to do it in 1.9 and not 1.07
    thanks!

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