Question: Readdepth And Exome Sequencing.
1
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

I'm trying to use readdepth with exome sequencing data.

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

  • Can I use readdepth with exome sequencing data ?
  • should remove/mask all the genomics segments that shouldn't be captured (=only keep the exon data) ?
  • how can I tell readdepth to ignore the regions having a low coverage ? For example, the following region was reported by readdepth:

:

26446481  26446491  26446501  26446511  26446521  26446531  26446541  26446551  26446561  26446571  
gaaaaaaaaaaaaggctgagcttgtggatgcgagccaaaagtgaatgctgctaccttactcagagaacaccttgaaagacagcagtaaatagaaatcctc
 ................................................                                                   
 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

:

R next-gen algorithm cnv sequencing • 1.6k views
ADD COMMENTlink written 7.1 years ago by Pierre Lindenbaum117k
3
gravatar for Chris Miller
7.1 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Hey Pierre,

For starters, you should probably read this answer I wrote up yesterday for Vikas: http://biostar.stackexchange.com/questions/17866/bias-during-exome-capture-for-cnv-analysis/17890#17890

What it says, in a nutshell, is that readDepth (and most other CNV tools) will not work for exome data. The exception that I know of is VarScan2, and that only works if a) you have a matched normal and b) That matched normal was processed in the same way at the same time as the test sample.

If you have more questions, let me know, and I'd be happy to add a more detailed explain.

ADD COMMENTlink written 7.1 years ago by Chris Miller20k

Thanks a lot Chris

ADD REPLYlink written 7.1 years ago by Pierre Lindenbaum117k
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