How to prepare the input file from a VCF file (cotaining SNP)

[kuangzhuoran]

Hi !
I have a phased VCF file (containing SNP; generated by GATK and phased by beagle);

[ChenJuiYANG]

Hi, there is a hidden function in vcftools can do this.

vcftools --gzvcf ${vcf} --chr ${chr} --phased --ldhelmet --out ${output}

The version I used is vcftools/0.1.16.
I said hidden function because this command is not on their manual.
Weird. I don't know why they didn't put on their manual, but it worked well to me. Hope this is useful to you as well.

CJ Yang