<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>

CC BY-SA 4.0
2023-11-01T23:35:05.903Z
Thank you very much for your answer with multiple options. I will look into these. ¡Gracias! :)
Sylvia Rodriguez
CC BY-SA 4.0
2023-10-29T16:32:34.087Z
2023-10-29T16:32:34.087Z
BigMistake
<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>

<r><genome><illumina><copy-number><snp-chip>
How to get cytoband and gene level copy number from genome wide SNP array copy number data?
# 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

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## 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! :)  

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