CNV detection from BAM files (mouse)

Hi everyone. I am a completely new user of Galaxy and unfamiliar with bioinformatics. I have 80 single cell mouse oocyte WGS samples, of which 60 are different treatment groups and 20 are the control. I want to figure out which of these (in bam file) has aneuploidy or copy number variation. I wasn’t able to figure it out using the tutorials. Any help is appreciated thanks.

Welcome, @Ed_Brown

We have a tutorial but it uses exome sequencing reads, not WGS. Hands-on: Somatic Variant Discovery from WES Data Using Control-FREEC / Somatic Variant Discovery from WES Data Using Control-FREEC / Variant Analysis

Other than that, try searching the tool panel with “cnv” or browse the Variant tutorials, or just that section of the tool panel.

The server hosts more options, including the CVNkit tool suite. Scroll to the bottom of any of the tool forms to find the associated publication that includes a protocol that could be adapted for use with Galaxy (the authors directly reference Galaxy as a way to use these – and there may be a workflow already but I didn’t look close enough to find it, but you could :slight_smile: ).

If you find a protocol you want to follow, and have trouble adapting that to Galaxy, we can try to help more. Include the link to the protocol, and describe what you are having trouble with, along with your history if the data/technical parts seems relevant.

Hope this helps!