BaseRecalibrator/PrintReads BD and BI flags

genec

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!

Geraldine_VdAuwera

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.

genec

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

Geraldine_VdAuwera

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

genec

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.

wkretzsch

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