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chunk

Table of contents

  1. Description
  2. Usage
  3. Command line options
    1. Basic options
    2. Input files
    3. Window Parameters
    4. Model Parameters
    5. Output files

Description

Tool to create imputation chunks.

Usage

Simple run

GLIMPSE2_chunk --input file_chr20.bcf --map chr20.b38.gmap.gz --region chr20 --sequential --output chunks_chr20.txt

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 files

Option name Argument Default Description
-I [ --input ] FILE NA Reference or target dataset at all variable positions in VCF/BCF format. The GT field is not required
--region STRING NA Chromosome or region to be split
-M [ --map ] FILE NA Genetic map
--sparse-maf FLOAT 0.001 Expert setting. Rare variant threshold

Window Parameters

Option name Argument Default Description
--window-cm FLOAT 4.0 Minimal window size in cM
--window-mb FLOAT 4.0 Minimal window size in Mb
--window-count INT 30000 Minimal window size in #variants
--buffer-cm FLOAT 0.5 Minimal buffer size in cM
--buffer-mb FLOAT 0.5 Minimal buffer size in Mb
--buffer-count INT 3000 Minimal buffer size in #variants

Model Parameters

Option name Argument Default Description
--recursive NA NA Recursive algorithm
--sequential NA NA Recommended. Sequential algorithm
--uniform-number-variants NA NA Experimental. Uniform the number of variants in the sequential algorithm

Output files

Option name Argument Default Description
-O [--output ] STRING NA File containing the chunks for phasing and imputation
--log STRING NA Log file