VCFLD

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

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS

Erik Garrison and vcflib contributors.