Table of contents

1. Command line options
   1. Basic options
   2. Input files
   3. Output files

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Command line options

Basic options

Option name	Argument	Default	Description
--help	NA	NA	Produces help message
--seed	INT	15052011	Seed of the random number generator
-T [ --thread ]	INT	1	Number of thread used

Input files

Option name	Argument	Default	Description
-I [--input ]	STRING	NA	Genotypes of focal and reference individuals in VCF/BCF/ format
-H [--hole ]	STRING	NA	Genotypes of unrelated individuals in VCF/BCF/ format
-G [--group ]	STRING	NA	Group file listing focal and reference individuals
-M [--map ]	STRING	NA	Genetic map
-R [--region ]	STRING	NA	Target region

Output files

Option name	Argument	Default	Description
-O [--output ]	STRING	NA	Sum of HMM IBD probabilities per group TXT/VCF/BCF format
--ibd	STRING	NA	IBD segments per group
--scaffold	STRING	NA	IBD-based scaffold in VCF/BCF format
--log	STRING	NA	Log file