Realignment of Indels

I am planning to realign the indels in my BR corrected bam file. A useful idea?
If I want RealignerTargetCreator (RTC) and IndelRealigner(IR) to correct also my private indels do I have to leave out the options: --known and --consensusDeterminationModel -KNOWNS_ONLY.
Or only the last one.

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Hans, what do you mean by private indels? Do you have a list of indels that you would like to be considered for realignment? If so, you can add them with an additional --known argument.

  • Hi Geraldine, I want to avoid that the indels that are private (only) to my genome and not part of the 1000G_phase1.indels.b37.vcf indel are to left out.But I did run in between (without waiting for mummy's ok!) the RTC and the IR with both arguments.
    Is it likely that the new bam file will contain uncorrected indels?
    I am planning to call the variants of the IR corrected file with HC (and check again for possible HMM error).

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