RemoveNearbyIndels: CRSP

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Andrew Zhang

• May 13, 2020 06:49

 

"This is a preprocessing step for the CRSP sensitivity validation truth data"

what's the meaning of "CRSP",

Clinical Research Sequencing Platform (CRSP)?

https://gatk.broadinstitute.org/hc/en-us/articles/360036448952-RemoveNearbyIndels?flash_digest=0eaf67b717fb2669dae0a7f9a872b95918bc5456#

 

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  Andrew Zhang

  • May 13, 2020 06:49

  Not  a googlable question....

   

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  Bhanu Gandham

  • May 17, 2020 07:08

  Hi Andrew Zhang

   

  CRSP is the Broad Clinical Research Sequencing Platform. It was developed since they needed it and we made it available as part of the Mutect2 validation tools.

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  Andrew Zhang

  • May 17, 2020 07:21

  Hello Bhanu：

  Many thanks，I am wondering is it necessary to remove nearby INDEL，when I was trying to get the de novo  mutation using HaplotypeCaller.

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  Bhanu Gandham

  • May 18, 2020 01:10

  Hi Andrew,

   

  Depends on your experimental design and what it is that you are trying to do. Can you explain that a little more?

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  Andrew Zhang

  • May 18, 2020 01:17

  Hi Bhanu,

  It is to use the candidate list currently obtained through the VCF file of the parents and child. Then through some reasonable steps, reduce the false positive rate of spontaneous mutations, thereby reducing the workload of subsequent experimental verification.

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  Bhanu Gandham

  • May 18, 2020 18:16
  • Edited

  Hi Andrew Zhang

   

  We do not recommend using this tool. This was developed for a very specific internal purposes only. 

   

  Going forward we are going to make it very clear in our documentation that this is not for external use.

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