Mutect2 for Pool-seq ?

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Loïc Quevarec

• June 11, 2021 12:49

Hello all,

I want to study the genetic diversity (SNP) in a population of nematodes (Caenorhabditis elegans). As the organism is small (less than 1 mm), we pool a lot of individuals to have enough DNA to prepare the libraries, we talk about PoolSeq. Another problem is that it is difficult to know the exact number of individuals placed in the pool, and thus ploidy.

I was wondering if Mutect2 could be adapted in this case, I assuming that searching for variants within a nematode population pooled could be similar to searching for variants among a cancer cell population.
I wanted to have your opinion on this approach, does it seem like a good idea to proceed this way?

Thank you !
Loïc

 

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  Bhanu Gandham

  • June 14, 2021 14:36

  Hi ,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the non-human topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Bhanu

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  Genevieve Brandt (she/her)

  • July 19, 2021 19:57

  Hi Loïc Quevarec,

  Yes, Mutect2 would be the best option for this case. Thanks for writing in with your question!

  Best,

  Genevieve

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  Loïc Quevarec

  • July 20, 2021 07:34

  Hi,

  Thank you very much for your help !

  Best regard,

  Loïc

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