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BD and BI tags and the SAM spec

TechnicalVaultTechnicalVault Cambridge, UKMember

Do you guys have any plans to get BD and BI tags added to the SAM spec?

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Answers

  • TechnicalVaultTechnicalVault Cambridge, UKMember

    The reason I ask is that I'm currently researching the purity filtering and recalibration we do here at the Sanger. It uses the tagged spiked in PhiX to recalibrate the quality scores, and I was thinking about whether it would be worth it how hard it would be to extend it to implement BD and BI scores. I'm also trying to figure out how it interacts with BQSR and trying to figure out whether it's a good or bad thing to do both. Also it looks like a new version of the SAM spec might be tagged in response to the abilities of the new BWA algorithm.

  • CarneiroCarneiro Charlestown, MAMember

    @rpoplin is going to get in touch with you to discuss this topic in more detail. We are still treating this as a research topic and we have other approaches that are being evaluated before we set on the standard of having 3 strings of base qualities.

  • HollyHolly UKMember

    Could you please advise in GATK v3.4, does the UG and HC still uses BI and BD tags? Any other possible downstream applications would need BD and BI? If these tags are not used downstream anymore, can be stripped to save some space.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Holly
    Hi,

    The BD and BI tags are the indel base qualities added by BQSR. They are still used by GATK, so you should not get rid of them.

    -Sheila

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