Question: Detection of CNVs
0
gravatar for nkausthu
2.6 years ago by
nkausthu20
nkausthu20 wrote:

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 • 831 views
ADD COMMENTlink modified 2.6 years ago by chen1.9k • written 2.6 years ago by nkausthu20
0
gravatar for WouterDeCoster
2.6 years ago by
Belgium
WouterDeCoster39k wrote:

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,...)

ADD COMMENTlink written 2.6 years ago by WouterDeCoster39k

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

ADD REPLYlink written 2.6 years ago by nkausthu20
0
gravatar for chen
2.6 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

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

ADD COMMENTlink written 2.6 years ago by chen1.9k

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?

ADD REPLYlink written 2.6 years ago by nkausthu20

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by chen1.9k

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

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.

ADD REPLYlink written 2.6 years ago by chen1.9k

Thank you so much ...

ADD REPLYlink written 2.6 years ago by nkausthu20
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