Answers.Body: <p>To obtain cytoband and gene-level copy numbers from genome-wide SNP array copy number data, you might want to consider using the ASCAT tool, as it makes allele-specific copy number segment data and derived integer gene-level copy number values from SNP array data. The SNP6 copy number analysis pipeline (ASCAT2) I believe is specifically for this purpose.</p>
  <p>See also:</p>
  <ul>
  <li><p>CNVkit, which has a method for copy number detection via using targeted reads and the non-specifically captured off-target reads to infer copy number evenly across the genome.</p>
  </li>
  <li><p>Array Comparative Genomic Hybridization (aCGH) and SNP Genotyping Technologies</p>
  </li>
  <li><p>CNVannotator</p>
  </li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-01T23:35:05.903Z
Answers.Text: Thank you very much for your answer with multiple options. I will look into these. ¡Gracias! :)
Answers.UserDisplayName: Sylvia Rodriguez
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-29T16:32:34.087Z
Answers.LastActivityDate: 2023-10-29T16:32:34.087Z
Answers.UserDisplayName: BigMistake
Body: <p>I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).</p>
  <p>What tool(s) can I use to get the integer copy numbers (either -3 to +3 or 0 to inf) for each cytoband and for each gene in the genome?</p>
  <p>I assume that people routinely do this? Are there any R packages/pipelines/code to do this?</p>
  <p>Do people use <code>DNAcopy</code> and/or <code>GISTIC</code> for this?</p>
  <p>Thank you.</p>
  
Tags: <r><genome><illumina><copy-number><snp-chip>
Title: How to get cytoband and gene level copy number from genome wide SNP array copy number data?
ThreadText: # How to get cytoband and gene level copy number from genome wide SNP array copy number data?
  
  (Asked by: username_0 on 2023-09-13)
  
  I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
  
  What tool(s) can I use to get the integer copy numbers (either -3 to +3 or 0 to inf) for each cytoband and for each gene in the genome?
  
  I assume that people routinely do this? Are there any R packages/pipelines/code to do this?
  
  Do people use `DNAcopy` and/or `GISTIC` for this?
  
  Thank you.
  
  **Tags:** r, genome, illumina, copy-number, snp-chip
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-10-29. Score: 3 | Accepted answer
  
  To obtain cytoband and gene-level copy numbers from genome-wide SNP array copy number data, you might want to consider using the ASCAT tool, as it makes allele-specific copy number segment data and derived integer gene-level copy number values from SNP array data. The SNP6 copy number analysis pipeline (ASCAT2) I believe is specifically for this purpose.
  
  See also:
  
  * CNVkit, which has a method for copy number detection via using targeted reads and the non-specifically captured off-target reads to infer copy number evenly across the genome.
  * Array Comparative Genomic Hybridization (aCGH) and SNP Genotyping Technologies
  * CNVannotator
  
  > **Comments:**
  > **username_0**: Thank you very much for your answer with multiple options. I will look into these. ¡Gracias! :)  
  
  ---
  
  