---
title: Why did my CGH microarray analysis fail or show CNVs in the wrong place?
description: CGH microarray analysis failed or CNVs in the wrong place? Check that your project's genome matches your Agilent export files, then relaunch.
---

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# Why did my CGH microarray analysis fail or show CNVs in the wrong place?

## Learn why a genome build mismatch between your CGH export files and your project breaks GermVar Tertiary analyses, and how to relaunch them.

The most common cause is a genome build mismatch: your CGH export files use one reference genome and your project uses the other. Relaunch the analyses in a project whose **Genome** matches the build of your files.

Applies to: GermVar Tertiary · CGH microarray (Agilent) · GRCh37 and GRCh38 · Main and Preview

### What you see

- The analysis fails, often for a sample with a CNV near the end of a chromosome, such as chromosome Y.
- Or it completes, but its CNVs show the wrong position, cytobands and genes, with no warning.

### Why it happens

Agilent CytoGenomics writes the genome build in the first line of each export file, for example `Genome: hg19`. SeqOne reads the CNV coordinates as they are and annotates them with the **Genome** of your project. It does not convert coordinates from one build to the other.

When the builds differ, an event can lie beyond the end of a chromosome in the project's build, and the analysis fails. The other events are annotated at the wrong position.

**Important:** Do not interpret the CNVs of an analysis whose project genome differs from its files. Delete these analyses if you can, or make sure nobody uses them.

### How to fix it

#### Check the build of your files

1. Open one IntervalBasedReport file in a text editor. Do not save it from Excel: this makes the file unusable.
2. Read the first line. `Genome: hg19` means GRCh37 (hg19); `Genome: hg38` means GRCh38.
3. In your project, compare it with **Genome** under **Meta-data**.

For the file names SeqOne accepts, see [What file formats can I use for tertiary aCGH analysis?](https://support.seqone.com/knowledge-base/what-file-formats-can-i-use-for-tertiary-acgh-analysis?hsLang=en)

#### Relaunch the analyses in a project with the right build

You cannot change the genome of a project after you create it. Create a new project instead.

1. Select **New project**.
2. On **2. Sequencing**, set **Sequencing method** to **CGH Micro array** and **Sequencing platform** to **Agilent**.
3. Set **Genome** to the build of your files, then select **Create project**.
4. In the new project's **Analyses** tab, select **Add Samples** and upload your files.
5. Select **New Analysis**, choose the workset and your samples, then select **Start analysis**.

**Note:** To keep your project, you can instead re-export the files in its genome build from Agilent CytoGenomics. Contact the Support team first.

**Tip:** Before you create a CGH microarray project, read the `Genome:` line of one export file and select the same build under **Genome**.

### If the problem persists

Send the Support team the project name, the analysis names and the first line of one export file.

**Still need help?** Contact our Support team at [support@seqone.com](mailto:support@seqone.com).

- [Troubleshooting](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#main-content)

    - [Error and info messages](https://hubspot.seqone.com/test_seqone/troubleshooting?hsLang=en#error-and-info-messages)

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