vcfld.md

% VCFLD(1) vcfld (vcflib) | vcfld (VCF transformation) % Erik Garrison and vcflib contributors

NAME

vcfld

SYNOPSIS

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

DESCRIPTION

Compute LD

OPTIONS

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

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

vcfld.cpp

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.