---
title: "Sanger indel spectrum (editing efficiency without NGS)"
method: POST
path: "/sanger_indel_spectrum"
tags: ["Alignment & variants"]
---

# Sanger indel spectrum (editing efficiency without NGS)

`POST /sanger_indel_spectrum`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/sanger_indel_spectrum`
- Auth: none required

Quantify CRISPR editing from a pair of Sanger traces — an unedited control and the edited pool — by decomposing the edited trace onto shifted copies of the control. Returns the indel spectrum (how much of the pool carries each insertion or deletion size), the unedited fraction, and the R² of the decomposition, which is the number that says whether the model fits your traces at all. Non-negative least squares, so no allele is ever assigned a negative share. Does not work for base editing, which makes a mixed base rather than a shift.

## Request body

- object
  - `controlBases` string, required: Base calls of the UNEDITED control read.
  - `controlChannels` array[], required: Per-base [A, C, G, T] intensities of the control read, one row per called base, read at that base's peak location (trace arrays are indexed by scan, not by base).
    - number[]
  - `editedBases` string, required: Base calls of the edited pool's read.
  - `editedChannels` array[], required: Per-base [A, C, G, T] intensities of the edited read, same convention.
    - number[]
  - `cutPosition` number, required: 1-based position of the expected cut, in CONTROL read coordinates.
  - `maxIndel` number: Largest indel to include in the basis, in bp (max 20). Every shift from −maxIndel to +maxIndel is fitted.
  - `windowLength` number: Bases downstream of the cut used for the decomposition (20-300). Longer is better conditioned but needs more clean read.
  - `guard` number: Bases skipped immediately after the cut, where the trace is least reliable.
  - `offset` number: Override the alignment offset between the reads. By default it is found from the base calls upstream of the cut, which is reported back along with the identity achieved.

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)