vcfld(1) · carta

Usage

vcfld –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file my.vcf -e -d -r

Compute LD

: required: t,target -- argument: a zero base comma separated list of target individuals corresponding to VCF columns required: b,background -- argument: a zero base comma separated list of background individuals corresponding to VCF columns required: f,file -- argument: a properly formatted phased VCF file required: y,type -- argument: type of genotype likelihood: PL, GL or GP optional: w,window -- argument: window size to average LD; default is 1000 optional: e,external -- switch: population to calculate LD expectation; default is target optional: d,derived -- switch: which haplotype to count "00" vs "11"; default "00", Type: transformation

3 releases since Debian 11 (Bullseye); the text changed 2 times.