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# BaseRecalibrator/PrintReads BD and BI flags

Member Posts: 8
edited January 2013

What are the BD and BI flags that get added to my bam files after base recalibration? They seem to consist of a long string of "N"s, and I'm trying to understand if that is correct.

Thanks!

Post edited by Geraldine_VdAuwera on
Tagged:

Hi Gene,

Those are insertion/deletion base qualities, where N=45, which is the default quality score for indels assigned by the BaseRecalibrator. So it looks like your reads are not getting recalibrated and are just maintaining the default original qualities.

Geraldine Van der Auwera, PhD

Hi Gene,

Those are insertion/deletion base qualities, where N=45, which is the default quality score for indels assigned by the BaseRecalibrator. So it looks like your reads are not getting recalibrated and are just maintaining the default original qualities.

Geraldine Van der Auwera, PhD

• Member Posts: 8

Thanks. Is this expected behavior, or does it mean that something is wrong with the recalibration?

If you're only getting Ns everywhere, there may be something wrong, because nothing is getting recalibrated. What's you're command line?

Geraldine Van der Auwera, PhD

• Member Posts: 8

I've looked at the quality strings and they do actually get changed, the few I spot checked mostly had individual characters decreased by an average of 5.

Looking at the command line, it seems that the --disable_indel_quals must be responsible. I'm not sure why I included this originally.

• Member Posts: 6

How are the BD and BI tags used downstream? Can I safely remove them if I am not using the UnifiedGenotyper to do genotyping?

• Montreal, QCMember Posts: 28

Hi, I have a similar question to this. How are those tags now used with the newest version of GATK? Are they really helping for INDELs detection?

Thanks a lot

@JCGrenier The indel qualities are taken into account by the variant callers (specifically, the pairHMM algorithm) when assessing the amount of evidence there is for a particular variant, in much the same way that base qualities are used to assess evidence for SNPs.

Geraldine Van der Auwera, PhD

• Montreal, QCMember Posts: 28

Thanks Geraldine. Is there any quick way to add again those tags if I removed them from the racalibrated file? Or should I reprocess my files from a step before the recalibration?