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# BAQ tag error

Member

Hi,

I ran print reads command with -baq option as recalculate. But while running UnifiedGenotyper, i am getting following error:

"BAQ tag error: the BAQ value is larger than the base quality"

I am running UnifiedGenotyper with -baq option as CALCULATE_AS_NECESSARY.

Can you please let me know the reason for above error.

Regards

Gaurav

Tagged:

What version of GATK are you using?

• Member

I am using GenomeAnalysisTK-2.3-9-ge5ebf34 version.

Can you please upgrade to the latest version (2.4) and try again? Also, before you do that you should validate your bam file (using Picard tools) to make sure there's nothing wrong with it.

• Member

I was looking at a bug "Fixing BQSR/BAQ bug". Could this be the problem for above error. Further, Can you please elaborate on the fix?

• Member

• Member

Further to narrow down the problem, the intermediate bam file constructed (after alignment around indels) before running PrintReads is running fine with Unified Genotyper. I am using following command while running PrintReads:

java -Xmx4g -Djava.io.tmpdir=temp -jar GenomeAnalysisTK-2.4-3-g2a7af43/GenomeAnalysisTK.jar -T PrintReads -baq RECALCULATE -BQSR $recal -o$o -R Human_Genome/ucsc.hg19.fasta -I $in 2>>$tid 1>>\$tid

Hope this helps.

I see -- that looks like a bug. Can you upload a snippet of your bam file so that we can reproduce the error locally? Instructions here:

• Member

folder uploaded in ftp server (BAQ_tag_error.tar.gz). Hope this will help.

• Member

Just pitching in that I'm seeing the same problem. I would of course be very happy to see a solution to the problem, but if this will not go straight into the repository I would also be very happy to know which commit caused this so that I can temporarily revert to a earlier state.

Thanks @Gaurav1983, I'll let you know when we have a fix.

Johan, unfortunately this was probably introduced during the transition to 2.4, and that represents so many commits that it would be difficult to track down. I expect it will be easier to just go ahead and fix quickly... And as soon as we get the fix we'll patch the repo, so the wait should be minimal.