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.TH "VCFLD" "1" "" "vcfld (vcflib)" "vcfld (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]vcfld\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfld\f[R] \[en]target 0,1,2,3,4,5,6,7 \[en]background
11,12,13,16,17,19,22 \[en]file my.vcf -e -d -r
.SH DESCRIPTION
.PP
Compute LD
.SH OPTIONS
.IP
.nf
\f[C]

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 \[dq]00\[dq] vs \[dq]11\[dq]; default \[dq]00\[dq],                                   


Type: transformation

\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.