table of contents
VCFLD(1) | vcfld (VCF transformation) | VCFLD(1) |
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¶
OTHER¶
LICENSE¶
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.
AUTHORS¶
Erik Garrison and vcflib contributors.
vcfld (vcflib) |