Call CNVs using gene positions

Question

[shinken123]

Hi Everyone,

I am wondering if someone knows a method to call CNVs only on specified positions. Maybe using a software that allows to include a bed file with gene positions or any other regions of interest. This, using whole-genome Illumina pair-end sequencing data aligned against a reference genome (bam or sam file). I am especially interested in to use read depth CNV detection algorithms. Thank you in advance.

[WouterDeCoster]

using sequencing Illumina read depth data

You probably want to be a bit more specific here.

[Amitm]

Hi, CNV analysis could be done using SNP array data or sequencing data (whole-exome/ genome). You haven't specified what type of data you are looking at, but guessing from your interest "to use read depth" you probably have sequencing data (?). In any case, normalization of signal (read-depth from all genomic regions examined) is needed before identifying CN segments. So, you would have to process the whole data (exome/ genome) and once you have the results (CN segments) you can overlap them (using bedtools or similar) to known coordinates of genes. In fact many tools use gene information (BED file) and give you the result in terms of genes. One good example is CNVkit. Have a look at the documentation.

[shinken123]

I added more info. Thanks.

[ATpoint]

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