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% HAPLRT(1) hapLrt (vcflib) | hapLrt (VCF genotype) % Erik Garrison and vcflib contributors

NAME

hapLrt

SYNOPSIS

hapLRT --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --type GP --file my.vcf

DESCRIPTION

HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. The sign denotes if the target has longer haplotypes (1) or the background (-1).

OPTIONS



Output : 4 columns :                             
     1. seqid                                    
     2. position                                 
     3. mean target haplotype length             
     4. mean background haplotype length         
     5. p-value from LRT                         
     6. sign                                     

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, GT or GP                                                  
optional: r,region     -- argument: a genomic range to calculate **hapLrt** on in the format : "seqid:start-end" or "seqid" 


Type: genotype

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

hapLrt.cpp

LICENSE

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