Body: <p>Could someone please explain the output file for HapFlk?</p>
  <p>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.</p>
  <p>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</p>
  <p>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</p>
  <ol>
  <li>nan for pvalue</li>
  <li>nan for flk and pvalue</li>
  <li>1.0 for pzero and nan for flk and pvalue</li>
  <li>0.5 for pzero and 0.0 for flk and 1.0 for pvalue</li>
  </ol>
  <p>I'm not sure how to interpret these positions cause the positions aren't missing in input ped file.</p>
  <p>Please help me</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-13T09:01:33.277Z
Comments.Text: crossposted https://www.biostars.org/p/9526800/
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-13T12:48:31.910Z
Comments.Text: 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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-13T18:43:02.750Z
Comments.Text: Regardless, you are likelier to get a good response to this at [Bioinformatics SE](https://bioinformatics.stackexchange.com) :).
Comments.UserDisplayName: gaspanic
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-14T04:47:27.847Z
Comments.Text: I'll keep that in mind thanks
Comments.UserDisplayName: Bionoob
Tags: <genetics>
Title: Could someone please help me understand the outputs for HapFlk
ThreadText: # Could someone please help me understand the outputs for HapFlk
  
  (Asked by: username_0 on 2022-06-13)
  
  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
  
  **Tags:** genetics
  
  > **Comments:**
  > **username_1**: crossposted https://www.biostars.org/p/9526800/  
  > **username_1**: 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.  
  > **username_2**: Regardless, you are likelier to get a good response to this at [Bioinformatics SE](https://bioinformatics.stackexchange.com) :).  
  > **username_0**: I'll keep that in mind thanks  
  
  ---
  
  ## 0 answers
  
  