Question: Convert GBS hapmap file into Plink bed file
gravatar for hd59430
2.6 years ago by
hd5943010 wrote:

Dear all,

I'm analyzing more than 200K SNPs across hundreds of diverse plant accessions. We got the data from GBS, so the raw SNP dataset is in hapmap format: column1: rs. (SNP name); column2: alleles; column3: chrom; column4: physical position in bp; column5: strand; column6: assembly; column7: center; column8: protLSID; column9: assayLSID; column10: panelLSID; column11: QCcode.

Then the following columns are different genotypes, and genotype data coded with IUPAC codes (A, C, G, T, R, S, Y, W, K, M).

I want to do a population structure analysis first and am planning to use ADMIXTURE software, which requires binary PLINK (.bed), or ordinary PLINK (.ped), or EIGENSTRAT (.geno) input file format.

Does anyone know how to convert GBS hapmap format into PLINK bed/ped format?


sequencing snp next-gen genome • 2.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by hd5943010
gravatar for hd59430
2.6 years ago by
hd5943010 wrote:

OK, in case anyone has similar questions. I figured it out.

  1. Convert GBS hapmap file to VCF; I did it in tassel: ./ -fork1 -h my_hapmap.hmp.txt -export -exportType VCF -runfork1

  2. Convert vcf file to plink format: vcftools --vcf input_data.vcf --plink --out out_in_plink

ADD COMMENTlink written 2.6 years ago by hd5943010
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