plotHaps.md

% PLOTHAPS(1) plotHaps (vcflib) | plotHaps (VCF statistics) % Erik Garrison and vcflib contributors

NAME

plotHaps

SYNOPSIS

DESCRIPTION

plotHaps provides the formatted output that can be used with 'bin/plotHaplotypes.R'.

OPTIONS

Output : haplotype matrix and positions

**plotHaps**  --target 0,1,2,3,4,5,6,7  --file my.phased.vcf.gz                                                           

required: t,target     -- argument: a zero base comma separated list of target individuals corrisponding to VCF column s        
required: r,region     -- argument: a tabix compliant genomic range : "seqid:start-end" or "seqid"                          
required: f,file       -- argument: proper formatted phased VCF file                                                            
required: y,type       -- argument: genotype likelihood format: PL,GP,GP                                                        

Type: statistics

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

plotHaps.cpp

LICENSE

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