vcfld

       Erik Garrison and vcflib contributors.

vcfld (vcflib)                                                                                          VCFLD(1)

       Compute LD

0      Success

       not0  Failure

       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

vcfld

              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

vcflib(1)

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