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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?

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  • $\begingroup$ Hi! I am not so familiar with this output format. Could you explain what we are looking at in the output sample? $\endgroup$
    – winni2k
    Nov 12, 2023 at 7:12
  • $\begingroup$ @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? $\endgroup$
    – Alice Yan
    Nov 12, 2023 at 8:47
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    $\begingroup$ 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? $\endgroup$
    – terdon
    Nov 12, 2023 at 11:50
  • $\begingroup$ I would also recommend searching dbsnp for the kir mutations. $\endgroup$
    – winni2k
    Nov 13, 2023 at 9:11
  • $\begingroup$ your output file does not seem to match what is described in T1K docs. Are there other files output? T1K is supposed to output a VCF even. $\endgroup$ Nov 13, 2023 at 20:48

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