AddOrReplaceReadGroups.jar --RGLB

NickNick Member
edited March 2015 in Ask the GATK team

I have 16 libraries that were pooled and sequenced on the same lane. When using AddOrReplaceReadGroups.jar, should I create a unique RGLB name for each library (e.g., lib1, lib2, lib3, etc.)? Apologies if this sounds like a silly question, but I have seen folks on seq-answers use the same name (e.g., lib1) for the RGLB flag when libraries were sequenced on the same lane.

Thanks!

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Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    @Nick You can let the tool use the default value, no need to set it yourself unless you have strong feelings about what it should be.

    Next time, can I ask you to please post this as a new question? We like to keep unrelated questions in separate threads.

Answers

  • NickNick Member

    Thanks! One quick question re: IndelRealigner. I am not entirely positive what integer to give the -LOD flag. My dataset is high coverage (~70X), but freq of indels is expected to be low. Any hints or suggestions would be much appreciated.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    @Nick You can let the tool use the default value, no need to set it yourself unless you have strong feelings about what it should be.

    Next time, can I ask you to please post this as a new question? We like to keep unrelated questions in separate threads.

  • NickNick Member
    edited March 2015

    Sorry! Will do.

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