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Table of contents

  1. Description
  2. Usage
  3. Command line options
    1. Basic options
    2. Input parameters
    3. Output files


Tool to create a binary reference panel for quick reading time.


Simple run

GLIMPSE2_split_reference --input-region chr20:7702567-12266861 --output-region chr20:7952603-12016861 --output binary_reference_panel --reference reference_panel_full_chr20.bcf --map chr20.b38.gmap.gz --threads 4

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 [ --threads] INT 1 Number of threads

Input parameters

Option name Argument Default Description
-R [--reference] FILE NA Haplotype reference panel in VCF/BCF format
-M [ --map ] FILE NA Genetic map
--input-region STRING NA Imputation region with buffers
--output-region STRING NA Imputation region without buffers
--sparse-maf FLOAT 0.001 Expert setting. Rare variant threshold
--keep-monomorphic-ref-sites NA NA Expert setting. Keeps monomorphic markers in the reference panel (removed by default)

Output files

Option name Argument Default Description
-O [--output ] STRING NA Prefix of the output file (region and extension are automatically added)
--log STRING NA Log file