Body: <p>I have a challenge with how to correctly code indels in plink (I plan to convert my binary file set to VCF and use it for lift over in downstream analysis).</p>
  <p>For instance, my dataset has an indel with rsID rs72552763 and, alleles ATGAT and AT. Its position is chr6: 160139849 - 160139853 (GRCh 38.p14).</p>
  <p>In the .map file, which bp position should I indicate?</p>
  <p>With respect to the .ped file, how should I code the alleles/genotypes?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-25T13:05:49.663Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-25T15:08:07.127Z
Comments.Text: Welcome to the site. I would simply recommend referring to the manual https://www.cog-genomics.org/plink/ and https://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf . There is plenty of information on both .ped and .map therein to address format concerns, in addition there will be reproducible examples. It would be useful to specify the sort of command you wish to run e.g. `plink --dosage myfile.dat --fam mydata.fam --map mymap.map`.
Comments.UserDisplayName: M__
Tags: <vcf><plink><indel>
Title: Correctly coding indels for ped/map files in plink and VCF
ThreadText: # Correctly coding indels for ped/map files in plink and VCF
  
  (Asked by: username_0 on 2023-07-25)
  
  I have a challenge with how to correctly code indels in plink (I plan to convert my binary file set to VCF and use it for lift over in downstream analysis).
  
  For instance, my dataset has an indel with rsID rs72552763 and, alleles ATGAT and AT. Its position is chr6: 160139849 - 160139853 (GRCh 38.p14).
  
  In the .map file, which bp position should I indicate?
  
  With respect to the .ped file, how should I code the alleles/genotypes?
  
  **Tags:** vcf, plink, indel
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Welcome to the site. I would simply recommend referring to the manual https://www.cog-genomics.org/plink/ and https://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf . There is plenty of information on both .ped and .map therein to address format concerns, in addition there will be reproducible examples. It would be useful to specify the sort of command you wish to run e.g. `plink --dosage myfile.dat --fam mydata.fam --map mymap.map`.  
  
  ---
  
  ## 0 answers
  
  