split_reference
Table of contents
- Description
- Usage
- Command line options
- Basic options
- Input parameters
- Output files
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 |
| 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 |