Open kuangzhuoran opened 1 year ago
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
Hi ! I have a phased VCF file (containing SNP; generated by GATK and phased by beagle);