Question: Detecting copy number variants from whole-exome sequencing data
0
gravatar for Shicheng Guo
8 months ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Hi All,

  1. Which tool could provide the most accurate CNV calling to whole-exome sequencing data?
  2. Is there any publicly available data have both WGS and WEX to the same sample to be used for CNV calling evaluation.

Thanks.

cnv exome-seq • 274 views
ADD COMMENTlink modified 8 months ago by hafiz.talhamalik230 • written 8 months ago by Shicheng Guo8.3k
1

Probably better to use long read sequencing as truth set rather than short read wgs. Or maybe both.

ADD REPLYlink written 8 months ago by WouterDeCoster44k
1

as suggested earlier CNVkit is a very good and easy to use tool. I aslo recommend that

ADD REPLYlink written 8 months ago by hafiz.talhamalik230
3
gravatar for jared.andrews07
8 months ago by
jared.andrews076.2k
St. Louis, MO
jared.andrews076.2k wrote:
  1. I've really enjoyed CNVkit. It's very easy to use, has good visualizations, and good documentation. "Accuracy" is a hard thing to measure for copy number calling if interested in focal changes as well, but the results from it make sense and correspond with other methods I've used, like copyCat.
  2. 1000 Genomes has some samples with both.
ADD COMMENTlink modified 8 months ago • written 8 months ago by jared.andrews076.2k
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