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can I strip out BD/BI stings after creating gvcf in the new 3.1 workflow?

I'm wondering if it's ok to remove the bd/bi tags after haplotypecaller creates the gvcf, the increase bam size is a problematic, the computional cost of recreating them in a 'just in case' scenario isn't as bad as the on disk cost of them so i'm wondering if they are not used after the first gvcf is created from individual samples.


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I confess I'm a little confused -- do you mean you want to archive a version of the bam from which you removed the tags? If so, you may be better off just archiving an unrecalibrated version of the bams and redo the recalibration if/when you need them. That would be better than specifically removing the indel recalibration information. The tags are indeed not used downstream of calling once you have the GVCFs.

  • jamjam Member

    Thanks for the information. I'd thought the recalibrated base qualities would be useful to keep for evaluating snps in igv but storing just the realigned should still be clear enough to evaluate them.

  • jamjam Member

    Thanks Geraldine,
    I'm still working out a workflow as it were, doesn't look like igv displays the BD/BI tags in an interactive manner so long term display of the realigned sounds good.


  • mikedmiked Member


    Can somebody from the GATK support team confirm if the BI/BD tags are being used with HC ? I recall running HC on some BAMs without the tags ( we removed the tags to reduce the footprint ) and it didn't complain.

    Any response is appreciated.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    They're used if they're there; if not, HC uses a workaround. I don't remember off the top of my head how the workaround works, but as I recall, it's not quite as good as having the BI/BD tags. Though I could be wrong. Will check.

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