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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.

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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

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    $\begingroup$ Thank you very much for your answer with multiple options. I will look into these. ¡Gracias! :) $\endgroup$
    – Sylvia Rodriguez
    Commented Nov 1, 2023 at 23:35

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