<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>

CC BY-SA 4.0
2023-11-12T07:12:56.030Z
Hi! I am not so familiar with this output format. Could you explain what we are looking at in the output sample?
winni2k
CC BY-SA 4.0
2023-11-12T08:47:24.347Z
@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?
Alice Yan
CC BY-SA 4.0
2023-11-12T11:50:26.220Z
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?
terdon
CC BY-SA 4.0
2023-11-13T09:11:13.253Z
I would also recommend searching dbsnp for the kir mutations.
winni2k
CC BY-SA 4.0
2023-11-13T20:48:12.720Z
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.
Maximilian Press
CC BY-SA 4.0
2023-11-14T07:45:23.857Z
@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~
Alice Yan
CC BY-SA 4.0
2023-11-14T18:51:14.990Z
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.
Maximilian Press
CC BY-SA 4.0
2023-11-18T08:18:45.123Z
@MaximilianPress Thank you, i really appreciate ur advice.
Alice Yan
<vcf><gene><plink><genotyping><imputation>
Convert genotyping results to vcf or other plink formats
# 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=
##phasing=partial
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FILTER=
##FILTER=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
#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**: @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?  
> **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**: @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~  
> **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**: @MaximilianPress Thank you, i really appreciate ur advice.  

---

## 0 answers

