ligate
Table of contents
Description
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.
The input files can be listed in any order. Chunks are sorted by position within each contig, and contigs follow the contig order of the input headers, or the order in which they first appear in the list if the headers do not list all contigs. Consecutive chunks of a contig must overlap so that their phase can be aligned; GLIMPSE2_ligate warns when they do not.
Usage
Simple run
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 [ --threads ] | 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 |
| --compression-level | INT | 6 | Compression level for VCF/BCF output: 0 = none (still BGZF-framed and indexable), 1 = fastest, 9 = smallest. Ignored for plain .vcf output. |
| --log | STRING | NA | Log file |