Geno to VCF conversion

[TD-lab-Wu]

Hi, I have some data from David Reich Lab. I want to convert it into VCF file. Could you please guide me how can I do this. Here I attached a sample dataset.

sample_data.zip

Thanks in anticipation.

[josephresearcher]

hi
first convert by convertf to PACKEDPED format command:
convertf -p par.txt
par.txt create and edit:
genotypename: sample_data.geno
snpname: sample_data.snp
indivname: sample_data.ind
outputformat: PACKEDPED
genotypeoutname: sample_data.bed
snpoutname: sample_data.bim
indivoutname: sample_data.fam

Then

with PLINK 1.9
With command: plink --bfile sample_data --recode vcf --out sample_datanew

[liamxg]

Dear @josephresearcher,

how to convert snp file to fasta file?

[liamxg]

Dear @josephresearcher,

where to find the par.txt?