Alignment & variants

Mixed bases and the uncalled tail of a Sanger trace

Read a chromatogram for what the basecaller did not report: positions where a second dye is present under the called base (a heterozygote, or a contaminating template), and bases still visible in the scan past where base calling stopped. Both are arithmetic on the channel intensities already in the file — a ratio, and a peak position extrapolated from the median spacing — not a model. Returns the called sequence rewritten with IUPAC ambiguity codes, the extra bases, and every threshold that produced the answer. Takes the SCAN arrays, because the tail lies past the last peak location.

post/trace_secondary_peaks

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/trace_secondary_peaks
  • Auth: none required

Request body

baseCallsstring required

Base calls, e.g. from parse_sanger_trace.

peakLocationsnumber[] required

Scan index of each called base's peak — one per base call.

channelAnumber[] required

Full A channel, indexed by SCAN (not by base).

channelCnumber[] required

Full C channel, indexed by scan.

channelGnumber[] required

Full G channel, indexed by scan.

channelTnumber[] required

Full T channel, indexed by scan.

qualitynumber[]

Optional per-base Phred scores; echoed beside each mixed position.

mixedRationumber

Secondary/primary intensity ratio at which a position is reported as mixed (0-1 exclusive). A convention, not a measurement.

skipLeadingnumber

Bases at the read's start excluded from the mixed scan (0-1000). The dye blob lives here and lifts every channel; without this every read reports a wall of false heterozygotes at its start.

tailSignalToNoisenumber

How far above the measured noise floor a channel must sit before the tail extension calls it (1-100).

maxExtensionnumber

Most extra bases to call past the last called base (0-400). The cap is part of the method: peak positions are extrapolated and the extrapolation drifts.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.