split_reference
Table of contents
Description
Tool to create a binary reference panel for quick reading time.
Usage
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 |