Question: Call CNVs using gene positions
gravatar for shinken123
4 weeks ago by
shinken12380 wrote:

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.

sequencing cnvs read depth • 90 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by shinken12380

using sequencing Illumina read depth data

You probably want to be a bit more specific here.

ADD REPLYlink written 4 weeks ago by WouterDeCoster43k

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.

ADD REPLYlink written 4 weeks ago by Amitm1.9k

I added more info. Thanks.

ADD REPLYlink written 4 weeks ago by shinken12380

Please use ADD COMMENT/REPLY and leave the answer field for answers.

ADD REPLYlink written 4 weeks ago by ATpoint29k
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