CLI reference¶
All commands support -h/--help and a global -v/--verbose flag. Run bsaseq --help
for the authoritative, version-matched help text.
| Command | Description |
|---|---|
run |
Complete BSA analysis pipeline |
samples |
List sample names in a VCF |
plot |
Regenerate plots from existing output |
annotate |
Annotate candidates with snpEff |
check-snpeff |
Verify snpEff installation |
bsaseq run¶
Runs filtering, sliding-window analysis, region calling, optional annotation, and plotting.
Required
| Option | Description |
|---|---|
--vcf |
Input VCF (bgzipped recommended) |
--high-bulk |
High/mutant bulk sample name(s), comma-separated for multiple |
--low-bulk |
Low/wild-type bulk sample name(s), comma-separated for multiple |
--out |
Output prefix (files named {PREFIX}_*.tsv, etc.) |
Filtering
| Option | Default | Description |
|---|---|---|
--min-dp |
10 | Minimum read depth per sample |
--max-dp |
200 | Maximum read depth (excludes repeats) |
--min-gq |
20 | Minimum genotype quality |
--min-qual |
30 | Minimum variant QUAL |
Windows
| Option | Default | Description |
|---|---|---|
--window-size |
1000000 | Window width (bp) |
--step-size |
250000 | Step between windows (bp) |
--min-variants |
5 | Minimum variants per window |
Candidates and mode
| Option | Default | Description |
|---|---|---|
--z-threshold |
3.0 | Z-score cutoff for significant windows |
--mode |
recessive | Inheritance mode: recessive or dominant |
Plotting and annotation
| Option | Default | Description |
|---|---|---|
--plot / --no-plot |
plot | Generate visualization plots |
--plot-format |
both | png, pdf, or both |
--max-region-plots |
5 | Maximum regional zoom plots |
--annotate / --no-annotate |
no-annotate | Run snpEff on candidate variants |
--snpeff-db |
none | snpEff database (required with --annotate) |
--snpeff-mem |
4g | snpEff Java heap |
bsaseq run --vcf calls.vcf.gz --high-bulk mut --low-bulk wt --out results/run \
--mode dominant --z-threshold 2.5 --annotate --snpeff-db Arabidopsis_thaliana
bsaseq samples¶
List sample names in a VCF (use these with --high-bulk / --low-bulk).
bsaseq plot¶
Regenerate plots from a previous run's TSV outputs.
| Option | Default | Description |
|---|---|---|
--windows |
required | *_windows.tsv from a prior run |
--regions |
required | *_regions.tsv from a prior run |
--variants |
*_variants.tsv (enables regional/diagnostic plots) |
|
--out |
required | Output prefix |
--z-threshold |
3.0 | Threshold line on the plot |
--format |
both | png, pdf, or both |
bsaseq annotate¶
Annotate an existing candidates file with snpEff and rank genes.
| Option | Default | Description |
|---|---|---|
--candidates |
required | *_candidates.tsv from a prior run |
--snpeff-db |
required | snpEff database name |
--out |
required | Output prefix |
--snpeff-mem |
4g | snpEff Java heap |
bsaseq check-snpeff¶
Verify that snpEff is installed and callable.