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Known issue: parent detection on GBS data

On GBS or DArTseq data of an F1 cross, CacaoIQ can miss the cross and keep Full unavailable. Choose the two parents yourself.

Some users with GBS or DArTseq genotypes of an F1 cross see CacaoIQ miss the cross, so Full analysis stays unavailable.

Status: Open, workaround available Affected: End-to-End Gene Discovery Full (linkage map and QTL) and the parentage (off-type) check, on sequencing-based genotypes (GBS, DArTseq) of one F1 cross Last updated: 2026-10-14

Symptoms

After you upload the genotype file of a biparental cross:

  • The Parents setting in the run panel is empty.
  • The note “Looks like one biparental cross” doesn’t appear.
  • Full stays unavailable, with the message:
Full needs both parents of a biparental cross (below).

Quick analysis still works.

Cause

Sequencing-based genotypes carry more genotyping errors than SNP-chip data. The automatic check for a biparental family is strict about those errors, so on GBS and DArTseq files it often fails to recognize a real cross.

Workaround

Choose the parents yourself:

  1. In the run panel, click Add the parents of a biparental cross.
  2. Pick the Female (seed) parent and the Male (pollen) parent from your samples.

Full then becomes available. The run’s own parentage check, which flags offspring that don’t fit the two parents, uses the thresholds in the run panel’s Genotype QC row. You can adjust them there.

If the results warn “Check the parents”, confirm that you picked the right two samples before using the results.

Fix timeline

Under investigation. This article will be updated when a version with a fix is available.

Updates

  • 2026-10-13: Article published. Issue open; workaround available.

Still stuck? Write to support@scilytics.ai with your system and what you see on screen. Don’t attach data files. The first reply comes within 2 business days.