snipe qc
Compute quality-control metrics for sample signatures against a reference.
snipe qc [OPTIONS]Options
Section titled “Options”| Flag | Type | Required | Default | Description |
|---|---|---|---|---|
--reference | text | yes | — | Reference .snipesig signature file. |
-o, --output | text | yes | — | Output TSV file for QC results. |
--sample | text | no | — | Sample .snipesig signature file path(s) (repeat for multiple; mutually exclusive with —samples-list). |
--samples-list | text | no | — | File listing sample .snipesig paths, one per line (mutually exclusive with —sample). |
--roi-sig | text | no | — | Optional region-of-interest .snipesig signature (K1-only SnipeSignature); mutually exclusive with —roi-bed. |
--roi-bed | text | no | — | Optional region-of-interest BED of genomic intervals, resolved against the reference’s stored coordinates (reference must be a sketch --genome signature); mutually exclusive with —roi-sig. |
--ychr | text | no | — | Optional Y chromosome .snipesig signature file (for samples missing Y). |
--var | text | no | — | Optional variance signature file(s) for contamination detection (repeat for multiple). |
--advanced | flag | no | off | Include verbose-tier metrics in the output. |
--hidden | flag | no | off | Include hidden developer-only metrics (not shown in help). |
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