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Could someone please explain the output file for HapFlk?

My input file was a ped file which has three different populations. Two with same number of snps by imputation and third one is an outgroup population which has the same number of snps but some of them are marked as 0 since it's missing and unimputed.

I ran HapFlk with only the --file and --outgroup option so the output would be Flk not the LD based HapFlk and outgroup would be leftout after building the tree

When I checked the flk result after running, the columns were rs, chr, pos, pzero, flk, pvalue which I could understand but some of the positions have

  1. nan for pvalue
  2. nan for flk and pvalue
  3. 1.0 for pzero and nan for flk and pvalue
  4. 0.5 for pzero and 0.0 for flk and 1.0 for pvalue

I'm not sure how to interpret these positions cause the positions aren't missing in input ped file.

Please help me

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    $\begingroup$ crossposted biostars.org/p/9526800 $\endgroup$
    – user438383
    Jun 13 at 9:01
  • $\begingroup$ I'm sorry , it's not allowed to crosspost? $\endgroup$
    – Bionoob
    Jun 13 at 10:39
  • 2
    $\begingroup$ It’s not against the rules, but it’s typically seen as polite to comment that you’ve posted elsewhere, to avoid people duplicating answering effort. $\endgroup$
    – user438383
    Jun 13 at 12:48
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    $\begingroup$ Regardless, you are likelier to get a good response to this at Bioinformatics SE :). $\endgroup$
    – gaspanic
    Jun 13 at 18:43
  • $\begingroup$ I'll keep that in mind thanks $\endgroup$
    – Bionoob
    Jun 14 at 4:47

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