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mourisl / T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
MIT License
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Convert KIR results to PLINK format #22

Open alicekiki opened 10 months ago

alicekiki commented 10 months ago

Hello,

I am very interested in your research. I found your method of using T1K to infer the KIR or HLA alleles from next-generation sequencing data very impressive and useful.

I have a question about how to convert the KIR results from T1K to PLINK format. The results contain sample ID and KIR alleles, and I want to perform some analyses on them using PLINK. However, I am not sure how to create a PED file and a MAP file from the KIR alleles generated by T1K.

Could you please advise me on how to convert the KIR results from T1K to PLINK format? I would appreciate any help or guidance from you.

Thank you for your time and attention.

mourisl commented 10 months ago

Could you please give me more details about the PLINK format you need?

alicekiki commented 10 months ago

I did the same conversion for HLA using HATK which generates a marker panel where the polymorphic variaiton of the HLA region, including SNPs and Amino Acid information, and it outputs bedbimfam files like this, i would like to know if there is any method to do this conversionfor KIR alleles. Thank you for your time~

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