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Strategies used by Genome Strip to detect CNVs

Dear all,

I'm only want to know which strategies are used by Genome Strip in order to detect the CNVs... I looking for in the Genome Strip web page but I'm not sure... I saw in different papers where they classify the detection using the Discordant Reads (RP), Read depth(RD). Another papers also include Split reads (SR) signals or even local assembly (AS).

So I will appreciate if you could clarify me which strategies used this tool...

Thanks for your help

Jordi
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Best Answer

  • bhandsakerbhandsaker admin
    Accepted Answer

    There are several different pipelines in Genome STRiP. The deletion discovery pipeline seeds on read pairs, then uses read depth in evaluation. Genotyping uses read pairs, split reads and read depth (although split read support in genotyping is limited in R2.0). The CNV discovery pipeline uses read depth find sites. Genotyping CNVs optionally uses read pairs if the bam/cram files are available, but only for copy number less then two. The LCNV (large/mosaic) CNV pipeline uses read depth exclusively.

    Some of this will change Genome STRiP R3.0. In particular, R3.0 makes more use of split reads during discovery and genotyping.

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Jordi_Valls

    I moved your question to the GenomeSTRiP category where @bhandsaker will help you.

  • Jordi_VallsJordi_Valls Member
    Thanks @bhanuGandham I will wait for response :smile:
  • Jordi_VallsJordi_Valls Member
    sorry @bhandsaker I know where is the web page, and I read the documentation and I dont find any place where explain which strategies use... or I dont find it. I see in the picture of the web page, different strategies, like RD, RP, BR( I dont know what does it mean BR) and LD (linkage desequilibrium I think), but in different papers are inconsistencies, like some paper say that Genome strip uses SR and another dont say this strategy and say de novo assembly. As I cannot clarify which strategies use Genome strip, I hope that you could tell me which signals use. I know that genome strip use RD and RP, but use another strategy?

    Thanks for your response...
  • bhandsakerbhandsaker Member, Broadie, Moderator admin
    Accepted Answer

    There are several different pipelines in Genome STRiP. The deletion discovery pipeline seeds on read pairs, then uses read depth in evaluation. Genotyping uses read pairs, split reads and read depth (although split read support in genotyping is limited in R2.0). The CNV discovery pipeline uses read depth find sites. Genotyping CNVs optionally uses read pairs if the bam/cram files are available, but only for copy number less then two. The LCNV (large/mosaic) CNV pipeline uses read depth exclusively.

    Some of this will change Genome STRiP R3.0. In particular, R3.0 makes more use of split reads during discovery and genotyping.

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