Readdepth And Exome Sequencing.

Question

[Pierre Lindenbaum]

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
 ................................................                                                   
 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

:

Answer 1

[Chris Miller]

Hey Pierre,

For starters, you should probably read this answer I wrote up yesterday for Vikas.

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.

[Pierre Lindenbaum]

Thanks a lot Chris