<p>What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well.</p>
<p>I'm working with leukemia sample and I have Illumina scan data ..in IDAT/GTC file format and i wish to use tools that will utilise the BAF and LRR metrics.</p>
<p>Microarray platform used- Illumina infinium 850K cytoSNP (beadchip array)</p>

CC BY-SA 4.0
2023-05-08T05:47:27.720Z
Maybe you can try karyoploteR. Great tutorial here: https://bernatgel.github.io/karyoploter_tutorial/
Sylvia Rodriguez
CC BY-SA 4.0
2022-04-11T14:20:20.877Z
What kind of analysis? What questions are you trying to answer? Should we assume human?
terdon
CC BY-SA 4.0
2022-04-12T15:15:32.177Z
@terdon I am trying to do CNV analysis...to detect copy number gains/loss and copy neutral loss of heterozygosity.... I'm working on acute lymphoblastic leukemia samples
newbiocoder
CC BY-SA 4.0
2022-04-12T16:07:40.667Z
Yes, I mean what kind of analysis? The word "analysis" suggests you aren't just trying to detect CNVs, but need to _analyse_ them. Maybe annotate them? Classify them according to the ACMG criteria? If you just want to detect them, that's a different issue.
terdon
<r><microarray><illumina><cnv>
open source tools for CNV analysis from illumina SNP array
# open source tools for CNV analysis from illumina SNP array

(Asked by: username_0 on 2022-04-09)

What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well.

I'm working with leukemia sample and I have Illumina scan data ..in IDAT/GTC file format and i wish to use tools that will utilise the BAF and LRR metrics.

Microarray platform used- Illumina infinium 850K cytoSNP (beadchip array)

**Tags:** r, microarray, illumina, cnv
> **Comments:**
> **username_2**: What kind of analysis? What questions are you trying to answer? Should we assume human?  
> **username_0**: @terdon I am trying to do CNV analysis...to detect copy number gains/loss and copy neutral loss of heterozygosity.... I'm working on acute lymphoblastic leukemia samples  
> **username_2**: Yes, I mean what kind of analysis? The word "analysis" suggests you aren't just trying to detect CNVs, but need to _analyse_ them. Maybe annotate them? Classify them according to the ACMG criteria? If you just want to detect them, that's a different issue.  
> **username_1**: Maybe you can try karyoploteR. Great tutorial here: https://bernatgel.github.io/karyoploter_tutorial/  

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## 0 answers

