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Table of contents

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


Ligatation of multiple phased BCF/VCF files into a single whole chromosome file. GLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.


Simple run

#ls -1v in order to keep the order within the chromosome
ls -1v chr20/*.imputed.bcf > list_imputed_files_chr20.txt

GLIMPSE2_ligate --input list_imputed_files_chr20.txt --output ligated_chr20.bcf --threads 2

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 threads

Input files

Option name Argument Default Description
-I [--input ] STRING NA Text file containing all VCF/BCF to ligate, one file per line

Output files

Option name Argument Default Description
-O [--output ] STRING NA Output ligated (phased) file in VCF/BCF format
--no-index STRING NA If specified, the ligated VCF/BCF is not indexed by GLIMPSE2 for random access to genomic regions
--log STRING NA Log file