success with exome sequencing?

[timodonnell]

I'm wondering if you or others have had success running PING from whole exome sequencing? Do the probes tend to capture enough KIR region reads or do they mostly get missed?

[n0rmski]

Dear Tim
I believe I may have been working (quite extensively) with your
  data for the last few months through Amir. 

Yes there is enough data captured and it will most likely work.
  The problem is that the exome capture method was designed using
  one reference genome.
I think this means ultimately that the coverage is not even -some
  alleles will produce more sequence reads than other alleles that
  are divergent from the reference.
The main consequence of this so far is on the gene content
  calling, because we use relative read depth to call the gene
  content/copy number.

The solution will be to run some controls -ie samples with known
  KIR alleles- through the exome capture method and then through the
  pipeline.
As with any experiment, without controls there remains an element
  of guesswork.
I hope this helps to clarify. Maybe we should talk directly if
  you need any further info or discussion.

All the best
Paul

On 21-Aug-18 9:40 AM, timodonnell
  wrote:

  I'm wondering if you or others have had success running PING
    from whole exome sequencing? Do the probes tend to capture
    enough KIR region reads or do they mostly get missed?
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-- 

Paul J Norman, PhD Associate Professor Division of Personalized Medicine, and Department of Immunology. Anschutz Medical School University of Colorado

[timodonnell]

Got it, this is very helpful. Thanks, Paul. We'll think some more and be in touch if we start to try these analyses.

Best,

Tim