Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-08T05:47:27.720Z
Comments.Text: Maybe you can try karyoploteR. Great tutorial here: https://bernatgel.github.io/karyoploter_tutorial/
Comments.UserDisplayName: Sylvia Rodriguez
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-11T14:20:20.877Z
Comments.Text: What kind of analysis? What questions are you trying to answer? Should we assume human?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-12T15:15:32.177Z
Comments.Text: @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
Comments.UserDisplayName: newbiocoder
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-12T16:07:40.667Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Tags: <r><microarray><illumina><cnv>
Title: open source tools for CNV analysis from illumina SNP array
ThreadText: # 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**: @username_2 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
  
  