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popgenmethods / LDhelmet

Software package for estimating fine-scale recombination rate.
GNU General Public License v3.0
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How to prepare the input file from a VCF file (cotaining SNP) #3

Open kuangzhuoran opened 1 year ago

kuangzhuoran commented 1 year ago

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

ChenJuiYANG commented 7 months 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