wisp
Documentation
About
Why population count masks?
Input modes
BAM/CRAM mode
All-sites VCF mode
Sparse output
Installation
Requirements
Conda environment
Verify the CLI
Build these docs locally
Arguments
Commands
Core arguments
Input-specific arguments
Shared optional arguments
BAM/CRAM mode options
Examples
Input files
Sample table for BAM/CRAM mode
Popfile for all-sites VCF mode
Sample and population labels
All-sites VCF
Variants-only VCF for BAM/CRAM mode
Threshold estimation
Variant exclusions
Mask BED
Examples
BAM/CRAM smoke run
Keep intermediate files
BAM/CRAM with a variants-only VCF
All-sites VCF run
Query the output
Overwrite existing outputs
Output files
Final outputs
BED columns
Metadata
Sparse interpretation
Intermediate files
Reference
Development
Set up a development environment
Run checks
Build documentation
Project layout
Implementation overview
API Reference
Configuration
AlignmentRunConfig
VcfRunConfig
Workflow
Samples
read_popfile()
read_samples()
Output summaries
Changelog
0.1.0
wisp
Index
Index
A
|
M
|
R
|
V
|
W
A
AlignmentRunConfig (class in wisp_mask.config)
M
module
wisp_mask.config
wisp_mask.samples
wisp_mask.summaries
wisp_mask.workflow
R
read_popfile() (in module wisp_mask.samples)
read_samples() (in module wisp_mask.samples)
V
VcfRunConfig (class in wisp_mask.config)
W
wisp_mask.config
module
wisp_mask.samples
module
wisp_mask.summaries
module
wisp_mask.workflow
module