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Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.

STAMPY and RealignerTargetCreator

jpofmarsjpofmars Posts: 2Member ✭
in Ask the team

Hello,

before I only used BWA and as you described in the best pratice I performed the realign step. Now I want to integrate in my pipeline Stampy associated with BWA.

Do you think, I should make the realign step ?

Thanks !

Post edited by Geraldine_VdAuwera on
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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 2,239Administrator, GSA Official Member admin

    I'm not familiar with the details of Stampy so I can't comment on it directly, but basically unless the aligner you use includes a step that specifically realigns reads around indels, doing the realignment step as per best practices is always recommended.

    Geraldine Van der Auwera, PhD

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