This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Detection of CNVs

After calculating each exon coverage using Depth of Coverage module in GATK, how to normalize each exon depth and calculate copy number ratio?

cnvs gatk
• 2,723 views • link
updated by chen chen • written by nkausthu • nkausthu

2 answers

There are multiple possible solutions. I would suggest having a look at published algorithms, and a good place to start would be https://omictools.com/cnv-detection2-category

More precisely, XHMM starts from coverage depth calculated by GATK. But there are multiple other tools (exomeCopy, codex, conifer,...)

• 0 views • link
written by WouterDeCoster WouterDeCoster

Thanks a lot and XHMM seems to a good option for me..

• 0 views • link
written by nkausthu • nkausthu

The key point of CNV detection is you have to make a baseline from controls, and do the normalization based on the baseline.

• 0 views • link
written by chen chen

As I want to find the CNVs from exomes of patients with Mendelian inheritance, any normal individual exome can be taken as a control? Does it make sense when two different patients are taken as control and normal?

• 0 views • link
written by nkausthu • nkausthu

You can use several healthy people's exomes as control.

• 0 views • link
written by chen chen

But the data has to be obtained by the same library prep (kit) and sequencer to be comparable.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Yes, so if you want to call CNV accurately, you have to sequence some healthy people with the same kit, using the same wet lab protocols.

• 0 views • link
written by chen chen

Log in to answer this question.

More posts like this