Geno to VCF conversion
TD-lab-Wu opened this issue · comments
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.
Thanks in anticipation.
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
Dear @josephresearcher,
how to convert snp file to fasta file?
Dear @josephresearcher,
where to find the par.txt?