GenomeStrip prepare summary metadata by chromosome?

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zzq

• May 25, 2020 01:18

Dear all,

 

To speed GenomeSTRiP, I want to SVPreprocess by chromosome. However, i am curious about the differences between the following two pipelines:  (1) run SVPreprocess by chromosome by setting "L", then run SVDiscovery and SVGenotyper without option "L"; (2) run SVPreprocess on whole genome, then run SVDiscovery and SVGenotyper with option "L". Hope you can help me and looking forward to your reply.

 

Sincerely, 

 

Zheng Zhuqing 

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  zzq

  • May 27, 2020 11:27

  Here attached the reply from Bob, hope can help you.

  Hi,

  Certainly we do #2 all the time, so that is definitely a well-known path. As to #1, I have not personally tried or benchmarked it. I do know that if you take the genome-wide quantities from preprocessing for one chromosome and compare them to a different chromosome or the whole genome, there can be deviations that will change the results.

  The main thing I would worry about are aneuploidies or perhaps large mosaic gains/losses that affect a large segment of a chromosome. This will distort the read depth estimation for that chromosome. If there is a large aneuploidy, this will also have small effect if you do #2, but because an aneuploidy on one chromosome is averaged with all of the others, the effect is usually small enough to not make much difference.

  Hope this helps,

  -Bob

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  Bhanu Gandham

  • May 28, 2020 18:21

  Hi Bob Handsaker

   

  Could you please take a look at this question. thank you!

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