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IndelRealigner known resources

aminziaaminzia aminziaMember

Hello there,

Would you please let us know how "IndelRealigner" makes use of "known" resources? I assume it already has the intervals of interest for realignment from the "RealignerTargetCreator". So it's not clear why it needs the resources again. Would it use them for making any sort of decision to reject or accept realigned indels?

Also, please let us know what happens (algorithmically) if we don't provide the same resources used in "RealignerTargetCreator" to the program.

Thank you
Amin Zia

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The known resources can be used for realignment. Depending on the option you select, reads within a target interval may be realigned to a known indel if present in the resources file, to indels present in the reads (in CIGAR strings), or using SW to generate alternate consensuses. This is described in the tool documentation here: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner.html#--consensusDeterminationModel

    Also, please let us know what happens (algorithmically) if we don't provide the same resources used in "RealignerTargetCreator" to the program.

    Do you mean if you provide no resources, or different resources?

  • aminziaaminzia aminziaMember

    Thank you for your reply.

    What I want to understand is whether the "known sites" is used by the IndelRealigner or the intervals that's computed based on these sites in the previous RealignerTargetCreator stage. If the former is true, why the program needs the known sites again as input parameter?

    Thank you again.

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