Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

STAMPY and RealignerTargetCreator

jpofmarsjpofmars Posts: 3Member
edited January 2013 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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