plotHaps1

Overview

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 status

0

Success

not 0

Failure

Other