Reg. Unified Genotyper error: BAQ tag error: the BAQ value is larger than the base quality
Posted in Ask the GATK team | Last updated on 2013-09-04 22:11:32


Comments (18)

Hello

We are working with canine whole genome and exome sequence data that has been aligned to canFam3.1. When we run the Unified Genotyper tool with the following option:

-T UnifiedGenotyper -baq CALCULATE_AS_NECESSARY -glm BOTH -nt 16 -R /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.fa -S SILENT -D /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.dbSNP.ens72.vcf -I AF23.jir.rc.bam -l INFO -o AF23.vcf -metrics AF23.gakt.metrics

we get the error message:

ERROR MESSAGE: SAM/BAM file SAMFileReader{/scratch/sswaminathan/canine_genomes_canfam3.1/alignments/AF23/AF23.jir.rc.bam} is malformed: BAQ tag error: the BAQ value is larger than the base quality

We also tried the following options:

-T UnifiedGenotyper -baq CALCULATE_AS_NECESSARY -fixMisencodedQuals -glm BOTH -nt 16 -R /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.fa -S SILENT -D /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.dbSNP.ens72.vcf -I AF23.jir.rc.bam -l INFO -o AF23.vcf -metrics AF23.gakt.metrics

and

-T UnifiedGenotyper -baq RECALCULATE -fixMisencodedQuals -glm BOTH -nt 16 -R /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.fa -S SILENT -D /scratch/sswaminathan/canine_genomes_canfam3.1/canFam3.1/canFam3.1.dbSNP.ens72.vcf -I AF23.jir.rc.bam -l INFO -o AF23.vcf -metrics AF23.gakt.metrics

but we receive the error message:

ERROR MESSAGE: Bad input: while fixing mis-encoded base qualities we encountered a read that was correctly encoded; we cannot handle such a mixture of reads so unfortunately the BAM must be fixed with some other tool

We are running The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29.

Could you please tell us what is the cause of this error and how we can rectify it?

Thank you Yours sincerely Shanker Swaminathan


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