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How to call indels in 454 data?

ChrisChris Member
edited August 2012 in Ask the GATK team

Hello!
I know GATK didn't call any indels in 454 data because the number of homozygous from 454 is not accurate. But how to call the true indels?? NO way with GATK??
Appreciate for your help!
Thx!

Best Answer

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    Hi Chris,
    Correct, there is no way to call indels with 454 data in the GATK (nor do we intend to implement such a capability).

  • ChrisChris Member

    ebanks said:
    Hi Chris,
    Correct, there is no way to call indels with 454 data in the GATK (nor do we intend to implement such a capability).

    Could you recommend some way to call indels in 454 data??

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You can post your question in "Ask the community" or actually your best bet is to ask on SeqAnswers.com, since there will probably be more people there who use other tools that might take 454 data.

  • ChrisChris Member

    Geraldine_VdAuwera said:
    You can post your question in "Ask the community" or actually your best bet is to ask on SeqAnswers.com, since there will probably be more people there who use other tools that might take 454 data.

    Sorry, I have posted only 1 time. I have known it!

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