ligate

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Description

Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.

Usage

Simple run

#ls -1v in order to keep the order within the chromosome
ls -1v chr1/*.phased.bcf > list_phased_files_chr1.txt

SHAPEIT5_ligate --input list_phased_files_chr1.txt --output ligated_chr1.bcf --thread 2

The program ligates together multiple phased files, listed in the input txt file (--input list_phased_files.txt) overlapping at buffer regions, using two threads (--thread 2), and saves the ouput file (--output ligated_chr1.bcf).

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 Text file containing all VCF/BCF to ligate, one file per line

Output files

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