Body: <p>I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can be used in plink?
  The file i have for now looks like this:</p>
  <pre><code>Gene_name Allele_1 Allele_2
  KIR2DL1 KIR2DL1*004 KIR2DL1*042
  KIR2DL4 KIR2DL4*005 KIR2DL4*005
  KIR3DL1 KIR3DL1*005 KIR3DL1*005
  KIR3DP1 KIR3DP1*006 KIR3DP1*010
  </code></pre>
  <p>My thought is to first convert the above file to a vcf file and use plink to generate bedbimfam from it, a standard vcf is like this:</p>
  <pre><code>##fileformat=VCFv4.3
  ##fileDate=20090805
  ##source=myImputationProgramV3.1
  ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
  ##contig=&lt;ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=&quot;Homo sapiens&quot;,taxonomy=x&gt;
  ##phasing=partial
  ##INFO=&lt;ID=NS,Number=1,Type=Integer,Description=&quot;Number of Samples With Data&quot;&gt;
  ##INFO=&lt;ID=DP,Number=1,Type=Integer,Description=&quot;Total Depth&quot;&gt;
  ##INFO=&lt;ID=AF,Number=A,Type=Float,Description=&quot;Allele Frequency&quot;&gt;
  ##INFO=&lt;ID=AA,Number=1,Type=String,Description=&quot;Ancestral Allele&quot;&gt;
  ##INFO=&lt;ID=DB,Number=0,Type=Flag,Description=&quot;dbSNP membership, build 129&quot;&gt;
  ##INFO=&lt;ID=H2,Number=0,Type=Flag,Description=&quot;HapMap2 membership&quot;&gt;
  ##FILTER=&lt;ID=q10,Description=&quot;Quality below 10&quot;&gt;
  ##FILTER=&lt;ID=s50,Description=&quot;Less than 50% of samples have data&quot;&gt;
  ##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=&quot;Genotype&quot;&gt;
  ##FORMAT=&lt;ID=GQ,Number=1,Type=Integer,Description=&quot;Genotype Quality&quot;&gt;
  ##FORMAT=&lt;ID=DP,Number=1,Type=Integer,Description=&quot;Read Depth&quot;&gt;
  ##FORMAT=&lt;ID=HQ,Number=2,Type=Integer,Description=&quot;Haplotype Quality&quot;&gt;
  #CHROM POS      ID         REF   ALT    QUAL  FILTER   INFO                             
  FORMAT       NA00001         NA00002          NA00003
  20     14370    rs6054257  G     A      29    PASS    NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ  0|0:48:1:51,51  1|0:48:8:51,51   1/1:43:5:.,.
  20     17330    .          T     A      3     q10     NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ  0|0:49:3:58,50  0|1:3:5:65,3     0/0:41:3
  20     1110696  rs6040355  A     G,T    67    PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ  1|2:21:6:23,27  2|1:2:0:18,2     2/2:35:4
  20     1230237  .          T     .      47    PASS    NS=3;DP=13;AA=T                   GT:GQ:DP:HQ  0|0:54:7:56,60  0|0:48:4:51,51   0/0:61:2
  20     1234567  microsat1  GTC   G,GTCT 50    PASS    NS=3;DP=9;AA=G                    GT:GQ:DP     0/1:35:4        0/2:17:2         1/1:40:3
  </code></pre>
  <p>Any tools can be used to realize it? For now i only have Gene names and allele names for each sample, How to obtain other genetic informtation a vcf file needed?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-12T07:12:56.030Z
Comments.Text: Hi! I am not so familiar with this output format. Could you explain what we are looking at in the output sample?
Comments.UserDisplayName: winni2k
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-12T08:47:24.347Z
Comments.Text: @winni2k Thank you for your reply. I have added more details to my question as you suggested. Could you please take a look at it again?
Comments.UserDisplayName: Alice Yan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-12T11:50:26.220Z
Comments.Text: I am not at all familiar with KIR genotyping, but is there a way of converting things like `KIR2DL1*042` into chromosome, position, ref and alt? Is there some database that lists what these KIR notations actually mean?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-13T09:11:13.253Z
Comments.Text: I would also recommend searching dbsnp for the kir mutations.
Comments.UserDisplayName: winni2k
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-13T20:48:12.720Z
Comments.Text: your output file does not seem to match what is described in [T1K docs](https://github.com/mourisl/T1K#inputoutput). Are there other files output? T1K is _supposed_ to output a VCF even.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-14T07:45:23.857Z
Comments.Text: @MaximilianPress  Thank you for reply. The output i posted is based on the genotype ouptput, The vcf output only contains noval SNP, i dont know how to obtain those info for other varients. Any methods to solve this? Thanks~
Comments.UserDisplayName: Alice Yan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-14T18:51:14.990Z
Comments.Text: Genotype output according to the docs looks like this: `gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2`. That doesn't match what you show. But regardless, if they really don't want to give you non-novel alleles there is likely a reason, I'd suggest contacting the authors on how you might do that. I glanced at the code but was not sure how to get non-novel, though [this line](https://github.com/mourisl/T1K/blob/master/VariantCaller.hpp#L138) might be relevant.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-18T08:18:45.123Z
Comments.Text: @MaximilianPress Thank you, i really appreciate ur advice.
Comments.UserDisplayName: Alice Yan
Tags: <vcf><gene><plink><genotyping><imputation>
Title: Convert genotyping results to vcf or other plink formats
ThreadText: # Convert genotyping results to vcf or other plink formats
  
  (Asked by: username_0 on 2023-11-11)
  
  I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can be used in plink?
  The file i have for now looks like this:
  
  ```
  Gene_name Allele_1 Allele_2
  KIR2DL1 KIR2DL1*004 KIR2DL1*042
  KIR2DL4 KIR2DL4*005 KIR2DL4*005
  KIR3DL1 KIR3DL1*005 KIR3DL1*005
  KIR3DP1 KIR3DP1*006 KIR3DP1*010
  
  ```
  
  My thought is to first convert the above file to a vcf file and use plink to generate bedbimfam from it, a standard vcf is like this:
  
  ```
  ##fileformat=VCFv4.3
  ##fileDate=20090805
  ##source=myImputationProgramV3.1
  ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
  ##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
  ##phasing=partial
  ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
  ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
  ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
  ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
  ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
  ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
  ##FILTER=<ID=q10,Description="Quality below 10">
  ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
  ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
  ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
  ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
  #CHROM POS      ID         REF   ALT    QUAL  FILTER   INFO                             
  FORMAT       NA00001         NA00002          NA00003
  20     14370    rs6054257  G     A      29    PASS    NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ  0|0:48:1:51,51  1|0:48:8:51,51   1/1:43:5:.,.
  20     17330    .          T     A      3     q10     NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ  0|0:49:3:58,50  0|1:3:5:65,3     0/0:41:3
  20     1110696  rs6040355  A     G,T    67    PASS    NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ  1|2:21:6:23,27  2|1:2:0:18,2     2/2:35:4
  20     1230237  .          T     .      47    PASS    NS=3;DP=13;AA=T                   GT:GQ:DP:HQ  0|0:54:7:56,60  0|0:48:4:51,51   0/0:61:2
  20     1234567  microsat1  GTC   G,GTCT 50    PASS    NS=3;DP=9;AA=G                    GT:GQ:DP     0/1:35:4        0/2:17:2         1/1:40:3
  
  ```
  
  Any tools can be used to realize it? For now i only have Gene names and allele names for each sample, How to obtain other genetic informtation a vcf file needed?
  
  **Tags:** vcf, gene, plink, genotyping, imputation
  
  > **Comments:**
  > **username_1**: Hi! I am not so familiar with this output format. Could you explain what we are looking at in the output sample?  
  > **username_0**: @username_1 Thank you for your reply. I have added more details to my question as you suggested. Could you please take a look at it again?  
  > **username_2**: I am not at all familiar with KIR genotyping, but is there a way of converting things like `KIR2DL1*042` into chromosome, position, ref and alt? Is there some database that lists what these KIR notations actually mean?  
  > **username_1**: I would also recommend searching dbsnp for the kir mutations.  
  > **username_3**: your output file does not seem to match what is described in [T1K docs](https://github.com/mourisl/T1K#inputoutput). Are there other files output? T1K is _supposed_ to output a VCF even.  
  > **username_0**: @username_3  Thank you for reply. The output i posted is based on the genotype ouptput, The vcf output only contains noval SNP, i dont know how to obtain those info for other varients. Any methods to solve this? Thanks~  
  > **username_3**: Genotype output according to the docs looks like this: `gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2`. That doesn't match what you show. But regardless, if they really don't want to give you non-novel alleles there is likely a reason, I'd suggest contacting the authors on how you might do that. I glanced at the code but was not sure how to get non-novel, though [this line](https://github.com/mourisl/T1K/blob/master/VariantCaller.hpp#L138) might be relevant.  
  > **username_0**: @username_3 Thank you, i really appreciate ur advice.  
  
  ---
  
  ## 0 answers
  
  